The hotel and restaurant operator Marriott Corporation completed Marriott's Great America on the site of what had been a pear orchard and opened it to the public on March 20, 1976. Admission was US$7.95 (equivalent to $44 in 2024) for adults (12 and up) and US$6.95 (equivalent to $38 in 2024) for children (4–11). There were 1,500 employees.

Less than two months later, on May 29, the company opened a second Marriott's Great America – later known as Six Flags Great America – north of Chicago in Gurnee, Illinois. A third park was initially planned for the Baltimore–Washington metropolitan area, but the idea was later abandoned after several failed attempts to sway local opposition.

The park, though profitable, was still an earnings disappointment for Marriott, leading the company in 1983 to explore options to sell. An interested party, Caz Development Co., appraised the land value at US$800,000 to $1 million per 1-acre (4,000 m2). Marriott also involved the city of Santa Clara in negotiations, which was already leasing 55 acres (22 ha) of parking space for the amusement park. Fearing homebuilding on the land by Caz Development would lower home values of existing homeowners, the city council approved a $101 million purchasing agreement on January 31, 1984, by a 4–3 vote that also had to be approved by city residents. The citywide vote passed, approving the sale by a margin of 3 to 1. Caz Development then sued the city and Marriott in the Superior Court of Santa Clara County to block the transaction. The court nullified the sale, forcing the city to attempt to salvage the deal through negotiations with the other parties.

Unable to broker a timely agreement, the city council voted 6–1 to scuttle the sale on February 5, 1985, though the city was still interested in owning the park. After Marriott refunded a $20 million down payment back to the city, negotiations were restarted. All parties were able to agree on a compromise, which was signed in marathon sessions taking place in early June 1985. The city acquired the park for $93.5 million from Marriott, which retained 20 acres (8.1 ha) from the sale for development. Caz Development settled and was allowed to build a hotel and office near the park, which the city renamed Great America.

Kings Entertainment Company, who owned and operated other amusement parks, was hired in 1985 to manage Great America for the city. In 1989, the city sold the park to Kings Entertainment, while retaining ownership of the land that the park occupied. In the agreement, the city would earn 5% of all revenue that exceeds $56 million.

Three years later, Paramount Communications (formerly Gulf+Western), the owners of Paramount Pictures, sought to join other entertainment companies as a theme park owner. The company acquired Kings Entertainment for $400 million on July 31, 1992, and created Paramount Parks. As part of the acquisition, Paramount purchased the parks owned by Kings: Great America, Kings Dominion, Carowinds, and a 20% stake in Canada's Wonderland; in addition, Paramount would acquire Kings Island, which was operated by Kings for its owner, American Financial Corporation. Viacom, the parent of MTV Networks (including Nickelodeon), then assumed control of Paramount in 1994 by purchasing a controlling interest, allowing Nickelodeon theming and merchandise into the park as well. During the Paramount era, attractions from the Action FX Theatre, Nickelodeon Splat City (later Nickelodeon Central), Drop Zone Stunt Tower, Invertigo, and many more modern thrill ride attractions were added in. Because the park is constrained from further expansion by its location in the center of Silicon Valley, several rides including the classic train ride and the Sky Whirl, a Marriott's Great America signature attraction, were removed to make way for newer attractions.

Viacom went on to acquire CBS in 1999, which made the combined Viacom/CBS the parent company of Great America and several broadcasting affiliates in the Bay Area, including KPIX-TV (CBS) and KBCW (UPN). Viacom/CBS split in 2005, with the re-formed CBS Corporation assuming control of Paramount Parks, until CBS sold that unit to Cedar Fair in 2006.

After Viacom and CBS Corporation split, Paramount Parks became a subsidiary of CBS. The theme park division was promptly put up for sale by CBS. In May 2006, Cedar Fair announced its acquisition of Paramount Parks.

Despite having a license agreement in place to retain Nickelodeon and Paramount branding for several years, Cedar Fair opted to remove them sooner. For the 2007 season, Paramount was dropped from the park's name, reducing it to Great America. The following season, Cedar Fair renamed it California's Great America in recognition of the park's original name. A Huss Rides top spin ride called FireFall was added that year, along with a new ice show in the Great America Theatre that was formerly called Paramount Theatre. Halloween Haunt, a Halloween-themed event held every weekend through the fall, also debuted at the park in 2008. The remaining Nickelodeon themes were replaced with characters and themes from Peanuts, a syndicated comic strip by Charles M. Schulz, for the 2010 season. The children's area was renamed Planet Snoopy. Similar changes were made at other Cedar Fair properties around the country.

On September 19, 2011, Cedar Fair confirmed reports that California's Great America would be sold to JMA Ventures, LLC for $70 million in cash. The sale required approval by the City of Santa Clara, and its city council was scheduled to vote on the matter on December 6, 2011. Cedar Fair, which purchased the park in 2006, expected to use the cash proceeds from the sale to reduce its senior secured debt. However, on December 6, 2011, JMA Ventures cancelled its plans to purchase the amusement park. In the same announcement, Cedar Fair also verified that a long-term agreement was reached with the San Francisco 49ers regarding parking and construction of a new stadium adjacent to Great America. Cedar Fair purchased the land beneath Great America from the city of Santa Clara in March 2019. The city retained the main parking lot in sale, which is shared between Levi's Stadium and Great America.

California's Great America did not operate in 2020 due to the COVID-19 pandemic and two stay-at-home orders issued by California Governor Gavin Newsom. It reopened on May 22, 2021, initially in a limited capacity, where face masks and social distancing were required. Also in 2021, the Boomerang Bay water park reopened as South Bay Shores, featuring new water slides in several areas of the park.

In June 2022, Cedar Fair announced the sale of the land occupied by California's Great America for $310 million to Prologis, a Bay Area logistics real estate company. Cedar Fair stated that the sale will help them lower the company's corporate debt to $2 billion, adding that they intended to close the park by 2033. The terms of the agreement involve Prologis leasing the land for an initial period of six years through June 30, 2028, with the option to renew the lease for an additional five years, although Prologis could terminate Cedar Fair's lease with as little as two years' notice. The mayor of Santa Clara, Lisa M. Gilmor, released a statement saying that the city only found out about the sale when the public did, that city officials planned to speak with Prologis to learn more details, and that the land is zoned for "theme park" use only.

In April 2023, the park updated its website to require visitors aged under 16 to be accompanied by a chaperone aged at least 21 in order to remain in the park after 4:00 pm.

On July 1, 2024, a merger of equals between Cedar Fair and Six Flags was completed, creating Six Flags Entertainment Corporation. It remained unclear how the merger would impact the scheduled closure of California's Great America in 2033.