Disney began planning a new park shortly after the opening of Disney-MGM Studios in 1989. Animal Kingdom was the brainchild of Imagineer Joe Rohde, who had previously designed the Adventurers Club at Pleasure Island. When presenting the idea of the new animal-themed park, Rohde brought a 400-pound (180 kg) Bengal tiger into the meeting with Disney CEO Michael Eisner. Originally slated as Disney's "Wild Animal Kingdom," Disney announced plans for the construction of the park in 1995 at an estimated cost of $600-$800 million. To design the theme park, Disney Imagineers traveled to Africa and Asia to study the landscapes and wildlife.

In July 1996, construction was underway on the animal holding facilities, the installation of trees, shrubs, and grasses to shape the park's African Savanna-inspired landscape. Disney Imagineers collected seeds from 37 countries to be used for the plants and grasses in the park. The landscaping efforts included spreading four million cubic yards of dirt, planting 40,000 mature trees (a mix of real Savanna species and artificial Baobab trees), constructing 60 miles (97 km) of underground utilities, and construction of various waterways, and structures built by over 2,600 construction workers. Many buildings contained thatched roofs assembled by Zulu workers from South Africa. About 1,500 hand-painted wooden horses were crafted in Bali under Disney supervision. Parts of the park were designed to have an aged appearance, with artificial potholes in the safari roads and boats peppered with dents and rust.

Most of the park's animals were acquired in 1997 during the fall; they were held at a rented holding facility in northern Florida for quarantine and observation. Disney hired staff from 69 zoos around the United States to care for the animals.

The park opened to the public on April 22, 1998. Several marketing events surrounded the day. ABC aired a two-hour prime time special about the making of Animal Kingdom, as part of its The Wonderful World of Disney anthology series. Eisner and Disney Vice Chairman Roy Disney hosted an opening day party for 14,000 corporate partners, travel agents, and media figures, which included celebrities such as Michael J. Fox, Drew Carey, Stevie Wonder, David Copperfield, and Jane Goodall. Broadcasts of Good Morning America, Today and Live with Regis and Kathie Lee aired live from the park on April 22.

In 2011, Disney announced a major expansion to the park, Pandora - The World of Avatar, a joint venture with director James Cameron and his production company, Lightstorm Entertainment, with the intention of transforming Animal Kingdom into a full-day operation with added attraction capacity and nighttime experiences. Construction on the area began on January 10, 2014, and the area opened to the public on May 27, 2017.

The park was closed from March 16 to July 11, 2020, due to the COVID-19 pandemic in Florida.

On September 9, 2023, it was announced at Destination D23 that DinoLand U.S.A. would be replaced with a new area inspired by the American tropics, and It's Tough to Be a Bug! would be succeeded by a Zootopia-themed film in the Tree of Life Theater.

On August 10, 2024, it was confirmed that It's Tough to Be a Bug! show would be replaced by the new show Zootopia: Better Zoogether in the Tree of Life Theater, opening in the winter of 2025, and DinoLand U.S.A. would be replaced by a new Tropical Americas land, set in the fictional town of Pueblo Esperanza, featuring Encanto and Indiana Jones-themed attractions with completion expected by 2027.

In October 2024, the closing date of DinoLand, U.S.A. was pushed to 2025. The first phase of the closure of DinoLand, U.S.A. became effective on January 13, 2025, with the closure of the subsection Chester & Hester's Dino-Rama, including TriceraTop Spin, Fossil Fun Games, and Chester & Hester's Dinosaur Treasures. In February 2025, it was announced that It's Tough to Be a Bug! would close on March 17, 2025.