In 1968, Sea World Inc. founder George Millay and his executives began looking for a place in Los Angeles county to build a theme park. Knowing that Newhall Land and Farming Company had enough undeveloped land in the new town of Valencia, he asked CEO John F. Dickason if they could build on his land. They eventually formed a partnership to build a 200-acre theme park. Construction began in November 1969 and continued until May 1971.

When the park opened, there were 500 employees and 33 attractions, many of which were designed and built by Arrow Development, which had previously worked on attractions at Disneyland. The admission price in 1971 was $5 for adults, and $3.50 for children between the ages of 3 and 12. Because the park was in a relatively remote part of Los Angeles County at the time, the Greyhound bus line provided bus service to and from the park and Los Angeles, as well as from Northern California, and optionally allowed purchase of park admission at the time the bus ticket was purchased.

At its 1971 opening, the rides and attractions included Gold Rusher, a steel coaster; the Log Jammer, a log flume; the Sky Tower, an observation tower; Grand Prix, similar to Disneyland's Autopia ride; El Bumpo, bumper boats; a carousel; and other smaller rides. There were four transportation rides to the peak: Funicular, a cable railway or funicular, which was renamed Orient Express, then Helpful Honda Express, and is currently named Magic Mover; The Metro, which consisted of three monorail stations around the park, including the Whitewater Lake, Country Fair, and Mountain stations; and "Eagles Flight", a gondola lift ride that had two stations at the peak, the long one north to Galaxy Station and the short one west to El Dorado Station. The Showcase Theater (later renamed the Golden Bear Theater) was part of the original park and featured Barbra Streisand as the first of many headline performers who would appear at Magic Mountain over the years.

In the 1971 season, Magic Mountain obtained permission from Warner Bros. to use Looney Tunes/Merrie Melodies characters. However, they did not continue using the characters after their first year (another Six Flags park, Six Flags Great America, has continuously used such characters since its opening in 1976, eight years before Marriott Corporation sold the park to Six Flags.) In 1972, Magic Mountain began using trolls as the park mascots. The trolls King Blop, also known as King Troll, Bleep, Bloop, and the Wizard became recognizable symbols of Magic Mountain. All King Productions, a contractor, provided the entertainers wearing the costumes until December 31, 1972, when Magic Mountain took on that role. The characters were used until 1985. Also in 1972, a second flume ride named Jet Stream was added.

In 1973, the park added its second roller coaster, the Mountain Express, a compact Schwarzkopf Wildcat model steel coaster. In 1974, the park also installed a new complex of spinning rides in what would later be known as Back Street. The new additions consisted of the Himalaya, Electric Rainbow, and Tumble Drum. In 1975, the Grand Centennial Railway opened in the Back Street. It took riders on a train journey to Spillikin Corners and back.

With the opening of Great American Revolution in 1976, Magic Mountain became the first park in the world to have a modern, 360-degree looping steel coaster (though previous roller coasters with loops had been built and dismantled elsewhere due to safety issues). When it was built, there was very little in the way of surrounding vegetation. In the time since, the tracks have been surrounded by trees and bushes, which prevents the riders from knowing the track layout beforehand. Universal filmed part of the suspense film Rollercoaster at Magic Mountain in late 1976, which featured the Revolution as its centerpiece during the film's climax.

In 1978, Colossus opened, and at the time was the fastest and largest dual-tracked wooden coaster in the world. Following its first season, it was closed and extensively redone. When it reopened, it was a much smoother ride. In 1991, the camel hump before the last, or third, turn was replaced by a block brake. Though it decreased the speed of the ride after this particular brake, it did allow three trains to run per side at a time, greatly increasing capacity. One of the trains sometimes ran backwards for a few years in the mid-1980s. However, until the late 1990s this kind of ride was no longer possible due to the newer ride system in place, as well as different trains. During Fright Fest, the park runs one side backwards using a set of trains acquired from the now-demolished Psyclone, which was located on the other side of the park. In 2015, the coaster was re-tracked with steel tracking and several inversions were added. It was subsequently rebranded "Twisted Colossus". This renovation was completed by Rocky Mountain Construction.

In 1979, the park was sold to Six Flags and became known as Six Flags Magic Mountain. In 1981, Six Flags Magic Mountain introduced Roaring Rapids, a river rapids ride that was on the West Coast for the first time. It was developed by Intamin in conjunction with the now-defunct Six Flags Astroworld, which had opened a similar ride in 1979. Along with Rapids came the completion of the midway near Spillikin Corners to link with Revolution's area. Finally, a complete circuit could be made around the park. It was originally designed as a dual-sided station, but only one was fully developed, and all that exists of the possible second side is a few supports. It uses large pumps to circulate water, and each of the two pumps can circulate 88,500 U.S. gallons per minute (5.58 m3/s). The reservoir can hold 1.5 million U.S. gallons (5.7 Ml) of water, and one of the innovations used on it was the introduction of guide boards to help eliminate jam ups.

In 1982, the attraction Freefall was added. Also built by Intamin, it was considered a cutting-edge drop tower ride if not strictly a "roller coaster." It simply ascends the tower and then drops down, with the track curving horizontally, leaving riders on their backs. Others were built for other parks (some of which are Six Flags). Today, most of these rides are obsolete and have been removed. Some flat rides were added, and others were removed the following year.

In 1984, Sarajevo Bobsleds was erected. Yet another ride built by Intamin, the coaster was basically a bobsled without ice and snow. The coaster was built in honor of the 1984 Winter Olympics, for which Sarajevo was the host city. Six Flags Great Adventure added a similar ride that same year. In 1986, Sarajevo Bobsleds was removed and now operates at Six Flags Over Texas as La Vibora. The other bobsled was moved to Six Flags Great America and later to The Great Escape in Queensbury, New York, where it operated as Alpine Bobsled.

In 1985, Children's World was rethemed as Bugs Bunny World, as Magic Mountain had abandoned the Trolls in favor of Looney Tunes/Merrie Melodies characters, licensed by Warner Bros. That year, Michael Jackson visited the park, riding rides such as Colossus, Revolution, and Roaring Rapids. In 1986, the park added a steel stand-up looping roller coaster called Shockwave, also designed by Intamin. This coaster was located in the back of the park, replacing Sarajevo Bobsleds. At the end of 1988, the coaster was removed as part of a ride rotation program and went to Six Flags Great Adventure in 1990. It was removed from there in 1992 and was repainted white and rethemed upon its removal to Six Flags Astroworld. There, it was known as Batman The Escape. When Astroworld closed in 2005, the ride was put in storage at Six Flags Darien Lake, where it remained until 2018, when it was finally sold for scrap.

In 1987, the park rethemed the Back Street. Spinning flat rides were renamed Turbo (Electric Rainbow), Subway (Himalaya), and Reactor (Enterprise). The dance club was rethemed as well and located near Reactor. After Hours, as it was now called (formerly Decibels), stayed open for one summer later than the rest of the park. It, along with Back Street, would remain open an additional two hours as a place for locals to hang out. This format lasted only one season.

In 1988, Ninja, "The Black Belt of Roller Coasters," opened. Built by Arrow Dynamics, it was the first suspended swing roller coaster on the west coast. Ninja has gone through very few changes since it was opened in 1988; evidently, only the wheels and paint have been changed.

Tidal Wave opened in 1989. It is a short, wet ride featuring a large boat that travels up a low-angled incline to a level water trough. The trough, in the shape of a semicircle, ends in a steep drop into a large splashpool. The impact displaces large amounts of water on its riders. The ride's exit ramp crosses over the splash pool, allowing willing patrons leaving the ride to get soaked from the splash. The attraction was closed to make room for Wonder Woman: Flight of Courage in 2020.

In 1990, Viper, a multiple-looping coaster designed by Arrow Dynamics, opened. It features a 188-foot (57 m) drop, speeds up to 70 mph (110 km/h), three vertical loops, a batwing turn that inverts riders twice, and a double corkscrew.

In 1991, Magic Mountain added Psyclone, a wooden coaster modeled after the Coney Island Cyclone. The Spillikin Corners area of the park was rethemed as Cyclone Bay to suit the new coaster, drawing guests into this area. The change was largely cosmetic, as the earlier theme relied on retail establishments that had been removed previously. The Shooting Gallery had replaced the Glass Blower, and the Candy Kitchen viewing area was redesigned. With Psyclone, the crowds returned. Psyclone's structure was damaged in the 1994 Northridge earthquake, and the ride was eventually removed in 2007. After adding Ninja, Viper, and Psyclone within four years, the park was building a large repertoire of big roller coasters.

A new coaster from Intamin called Flashback was added to the park the following year in 1992. The prototype Space Diver model was a first of its kind that had already operated at Six Flags Great America and Six Flags Over Georgia prior to its arrival. Due to the excessive noise it generated near Hurricane Harbor, Flashback was closed in 2003 and eventually removed in 2007.

In 1993, Six Flags Magic Mountain entered the Time Warner era. The new ride for the year was Yosemite Sam Sierra Falls, a water ride with two twisting tubes that riders could slide down using a raft. Also that year, there was retheming and the High Sierra Territory was opened. The Showcase Theatre became the Golden Bear Theater, the Animal Star Theatre was created in Bugs Bunny World, and a large, fake wooden tree was built. This year also saw the end of live non-Christian themed concerts in the park due to a riot that broke out as a result of a TLC concert that was oversold. Magic Mountain was quickly overwhelmed by large crowds that vandalized and destroyed property. Park shops had their windows broken and looting quickly followed. Police were called to the scene in full riot gear. The park was evacuated and closed down for the night.

In 1994, Magic Mountain added what two other Six Flags parks already had, a Bolliger & Mabillard inverted looping roller coaster called Batman: The Ride (more Six Flags parks also added the ride in the coming years). Batman: The Ride (BTR) is an inverted coaster, meaning the usual coaster protocol is reversed: the track is overhead and the cars are below it. The trains travel on the outside of the loops, and rider's legs hang freely, as on a ski lift.

A separately gated waterpark called Six Flags Hurricane Harbor opened on June 16, 1995. The 22-acre (8.9 ha) park included body slides, tube slides, a kiddie water play area, a lazy river, and a wave pool. The following year, a SkyCoaster called Dive Devil opened at Magic Mountain.

A dual launch coaster called Superman: The Escape debuted at the park on March 15, 1997. Designed by Intamin, the 30-second ride launches riders from 0 to 100 mph (160 km/h) in seven seconds on a track that scales up a 41-story tower. It was the first roller coaster in the world to reach speeds of 100 miles per hour (160 km/h). Originally slated to open in June 1996, the ride's opening was delayed and pushed back to 1997 as problems with the LSM launch motors were found. The tower structure was painted a grayish white when the ride first opened and lasted until 2011.

In 1998, a new Bolliger & Mabillard stand-up roller coaster called Riddler's Revenge opened as the tallest and fastest stand-up roller coaster in the world. Later that year, Six Flags was acquired by Premier Parks. In 2000, a steel hypercoaster called Goliath, which was manufactured by Giovanola, opened at the park.

Three new roller coasters opened in 2001, although only one opened on schedule – a kiddie steel coaster called Goliath Jr. The other two, Déjà Vu and X (now X²), suffered early mechanical issues. Déjà Vu opened late in 2001 and X opened early in 2002. Déjà Vu was designed by Vekoma and is a Giant Inverted Boomerang coaster (GIB), a variant of their popular Boomerang design. It is an inverted coaster with coaches suspended beneath an overhead track that traverses an open-circuit track forward and in reverse and features two completely vertical drops and three inversions. After its late opening, the ride still suffered a lot of downtime. X was designed by Arrow Dynamics as the world's first "fourth-dimensional" roller coaster. It was the only one in North America where riders experience going 360 degrees in their seats. Each seat lies on a separate axis from the track. This coaster managed to open briefly on January 12, 2002, only to close due to more technical problems. It reopened late in August of that year. The ride closed for a major refurbishment and retheme in 2008 where X transformed into X².

In 2003, Scream, designed by Bolliger & Mabillard, was added. At this point, Six Flags Magic Mountain tied with Cedar Point for the park with the most roller coasters in the United States. Scream is similar in concept to Medusa at Six Flags Discovery Kingdom and is a mirror image of Medusa at Six Flags Great Adventure. It is a floorless roller coaster with trains riding above the rails traversing seven inversions on 3,985 feet (1,215 m) of track on floorless trains. In 2006, Tatsu, a Bolliger & Mabillard flying roller coaster, was added, causing a temporary closure of Revolution and Roaring Rapids to allow construction to take place. It was much larger than the other three Bolliger & Mabillard Flying Coasters at other Six Flags parks, all named Superman: Ultimate Flight. Tatsu has a suspended-track orientation featuring vehicles that recline passengers with their backs against the track and facing the ground.

On June 22, 2006, Six Flags, Inc. announced that it was exploring options for six of its parks, including Magic Mountain and its neighboring water park, Hurricane Harbor. Though management said closing the park was unlikely, rumors still began that the park could be sold to real estate developers, with an intent to close the park and build housing developments in the area. Park officials cited dwindling attendance due to rowdy behavior among some of the park-goers as reasons for wanting to sell the park while management was wanting to move Six Flags into more of a family park direction. Throughout the Six Flags chain, attendance in the second quarter of 2006 was 14 percent lower than it was in the second quarter of 2005.

By the fall of 2006, Six Flags confirmed that Magic Mountain had remained for sale. They also stated, however, that it would be sold to a company that would continue to operate it as a park, and that closing Magic Mountain was not a possibility. Cedar Fair, Anheuser-Busch, and several others considered buying the park but none of the offers came close to the asking price.

By the time Six Flags announced which parks it was selling in January 2007, Magic Mountain was no longer one of them. The company decided not to sell Magic Mountain and its adjacent water park. Spokeswoman Wendy Goldberg said that upon further evaluation, the company decided that the Los Angeles parks remained too valuable to relinquish, as sales were increasing, and that the park would not be sold. Other parks were sold as a package and remained open.

With the removal of Flashback and Psyclone in 2007, Six Flags Magic Mountain was no longer tied for the record of having the most roller coasters in a single park, relinquishing the record back to Cedar Point. The park instead turned its focus to family-oriented improvements, including a new children's themed area called Thomas Town, which was added in 2008. One of its premier thrill rides received a makeover, however. X was closed on in late 2007 for its transformation into X2, adding new fourth-generation trains and special effects in addition to being repainted. It reopened on May 24, 2008. Later in 2008, the park also renovated the "Magic of the Mountain" museum at the top of its Sky Tower attraction, which houses memorabilia from the park's history including old television commercials, park maps, models, and equipment salvaged from defunct rides.

Terminator Salvation: The Ride, a wooden roller coaster, opened on May 23, 2009. It was built in the former location of Psyclone and featured tunnels, spraying mist, and special effects. On January 9, 2011, the ride was renamed Apocalypse and given an appropriate theme that reflects an "end of the world" scenario. Later that year, Six Flags President and CEO Mark Shapiro said in a Los Angeles Times published interview that Magic Mountain had plans to install a new roller coaster for its 2010 season, and would add a new themed area for children in 2011 called Wiggles World. Shapiro also stated that the adjacent Hurricane Harbor would receive an expansion.

On May 29, 2010, Mr. Six's Dance Coaster was scheduled to open but was delayed until 2011 when it would open under a new theme. On the same day, Mr. Six's Splash Island opened at the adjacent Hurricane Harbor water park.

On August 3, 2010, it was announced that Superman: The Escape would undergo a major redevelopment before the 2011 season. On October 20, 2010, Six Flags Magic Mountain officially announced their full plans for 2011 after a video was leaked six days earlier. In addition to opening Mr. Six's Dance Coaster under a new name and theme, Six Flags announced two other attractions. In time for the 2011 season, Superman: The Escape was refurbished to Superman: Escape from Krypton and opened on March 19, 2011. The coaster featured new backwards launching cars and a new color scheme. The third and final announcement regards an entirely new thrill roller coaster. Green Lantern: First Flight opened on July 1, 2011, as Magic Mountain's eighteenth roller coaster, which was an Intamin ZacSpin. With this roller coaster, Magic Mountain reclaimed for the park the world record for the highest number of roller coasters at a single theme park. It was later announced, on November 4, 2010, that the children's roller coaster would be called Road Runner Express and located in Bugs Bunny World.

In late 2010, Six Flags began the process of removing non-Warner Bros. licensed theming from attractions. They terminated several licenses including Terminator and Thomas the Tank Engine. Terminator Salvation: The Ride was renamed and rethemed into Apocalypse, which re-opened on January 8, 2011. Thomas Town was renamed and rethemed to Whistlestop Park in time for the 2011 season.

On January 18, 2011, the Los Angeles Times reported after considering a new theme based on DC Comics superhero sidekicks, the park opted for simplicity and renamed the Little Flash coaster to Road Runner Express. Due to Green Lantern being placed in Gotham City Backlot, the area was re-themed into DC Universe. In addition, Grinder Gearworks became "Wonder Woman: Lasso Of Truth" and Atom Smasher was renamed "The Flash: Speed Force".

In August 2011, several media sources reported that Six Flags New England would install Six Flags Magic Mountain's Déjà Vu for the park's 2012 season.

On September 1, 2011, Six Flags Magic Mountain announced that they would be opening a new attraction for the 2012 season named Lex Luthor: Drop of Doom. The free-fall drop attraction was integrated into both sides of the park's 415 feet (126 m) tall Superman: Escape from Krypton tower structure and ranks as the world's tallest drop tower, featuring a plummet from 400 feet (120 m) above ground level. The following day, Six Flags Magic Mountain confirmed on Facebook that Déjà Vu would be removed from the park. Then on September 13, 2011, the park announced that Déjà Vu would be removed after October 16, 2011, "Déjà Vu fans, we have created some exclusive after-hours ride time for you to ride it again before October 16."

On October 31, 2011, Log Jammer operated for the last time and was removed to make way for Full Throttle, which opened in 2013.

In August 2012, Six Flags Magic Mountain confirmed rumors that a new roller coaster, Full Throttle, would open the following season. Full Throttle opened as the park's 18th roller coaster, allowing Six Flags Magic Mountain to market having the most roller coasters in the world once again. The ride was built to feature the world's tallest vertical loop on a roller coaster at 160 feet (49 m). In addition, Full Throttle set a record for being the first roller coaster to feature a track section with rails on both sides of the spine. This occurs at the top of the ride's massive inversion.

On August 29, 2013, Six Flags Magic Mountain officially announced that they would run both Batman: The Ride and Colossus backwards for a limited time of the 2014 season. They will also expand Bugs Bunny World with the addition of a new roller coaster. On April 8, 2014, Six Flags Magic Mountain announced that the park will host its first ever Holiday in the Park Christmas event in late 2014 and for future years after.

In the summer of 2014, the park placed banners across the property advertising the Bonzai Pipelines in the adjacent property, Hurricane Harbor, along with the closing of Colossus which took place on August 16, 2014. On August 28, 2014, Six Flags announced the Rocky Mountain Construction conversion of Colossus into Twisted Colossus. Twisted Colossus opened on May 23, 2015.

On September 3, 2015, Six Flags announced the renovation of Revolution with a new paint scheme, upgraded lighting, and new train eliminating the controversial over-the-shoulder restraints that had been the source of the ride's spotty reputation for much of its life. Named "The New Revolution", the roller coaster reopened on April 21, 2016.

On September 1, 2016, the park announced Justice League: Battle for Metropolis to open in 2017. The 4D shooting dark ride is nearly identical to the six other installations located at Six Flags parks around North America. The ride opened on July 12, 2017, and is located in the Metropolis section near The Riddler's Revenge.

On August 29, 2017, Six Flags announced the addition of a Zamperla Giga Discovery flat ride to be built in a newly renovated Boardwalk Beach area near DC Universe. Marketed as "the world's tallest pendulum ride", CraZanity takes riders to a height of 172 feet (52 m) and speeds up to 75 miles per hour (121 km/h).

On August 29, 2018, the park announced the brand new racing launch coaster West Coast Racers from Premier Rides and a revamp of the old Cyclone Bay area into a high-energy, urban Los Angeles. The ride itself is dubbed the first launched racing coaster in the world and the first quadruple-launched coaster, even though the existing Fiorano GT Challenge holds these records. The Möbius loop coaster officially opened to the public on January 9, 2020, and became the 19th coaster at the park.

On March 24, 2019, the park announced that Green Lantern: First Flight would permanently close and be removed from the park which no longer makes West Coast Racers the park's 20th coaster.

On March 13, 2020, the park closed due to the COVID-19 pandemic. The theme park reopened on April 1, 2021, with Members and Passholders being granted access on April 1 and 2, with the general public being admitted to the park on April 3. As of August 2021, Six Flags Magic Mountain visitors are no longer required to wear masks outdoors.

On October 21, 2021, the park announced Wonder Woman Flight of Courage, the world's tallest and fastest single rail coaster, to open in summer 2022. The ride is an I-Box Raptor coaster built by Rocky Mountain Construction.

Starting November 1, 2022, the 365-day schedule, introduced in 2018 to "maximize travel industry opportunities", was limited to select weekends only during non-peak months. Park Marketing & Communications Publicist Alexandria French said in a statement that the changed operation schedule would deliver a more "exceptional guest experience".

In Spring 2023, Scream Break debuted at Magic Mountain, as well as Six Flags Over Texas, Six Flags Fiesta Texas, Six Flags Over Georgia, Six Flags Discovery Kingdom, Six Flags America, and Six Flags Great Adventure. The event lasted from March 18 through April 16 on Fridays, Saturdays and Sundays except for April 1–9. Hosted in the areas of DC Universe, Screampunk District, Full Throttle Plaza, and Six Flags Plaza, the event featured aspects of Fright Fest, such as themed props, shows, and mazes. Admission was available free for passholders on a first come, first served basis.

In early 2024, demolition work began on the Golden Bear Theater (Formerly Showcase Theater). After an incident at a TLC concert in the 90s, the theater sat dormant with the exception of the occasional regional cheer championship or religious gathering. A new Vekoma roller coaster is currently under construction, set to open in 2026, and will be built in and around the remnants of the Golden Bear Theater.