Plans for a second Disney park in Tokyo were first conceived in 1987, the same period when the "Law for the Development of Comprehensive Resort Areas" was passed. Initially, these plans included a park similar to Disney's Hollywood Studios (then Disney-MGM Studios), to be called Disney Hollywood Studio Theme Park at Tokyo Disneyland. This idea was later reconsidered in 1991 because of the economic collapse caused by Japanese asset price bubble. During the creation of the park, the Walt Disney Company and the Oriental Land Company had to compromise on certain design elements of the park due to cultural differences, such as the park's entrance focal point. The idea for what eventually became DisneySea was traced to a proposal to build a second theme park in Southern California called "Port Disney" in Long Beach, California, with the RMS Queen Mary as the main attraction. The idea was scrapped after Disney endured financial trouble with the Euro Disney project. Later the idea was passed on to the Oriental Land Company to expand their resort.

Ground for DisneySea was broken on October 22, 1998 and the park opened on September 4, 2001. Upon opening, Tokyo DisneySea became the ninth park of the twelve worldwide Disney theme parks to open.

In 2002 Tokyo DisneySea won a Thea Award from the Themed Entertainment Association for the concept, design, and construction of the theme park. The award was presented at El Capitan Theatre in Hollywood, California.

In October 2019, both Tokyo Disneyland and DisneySea were temporarily closed due to the threat of Typhoon Hagibis. On 28 February 2020, Oriental Land announced a temporary closure of Tokyo Disneyland and DisneySea from 29 February to combat the COVID-19 pandemic. The closure, originally slated to expire in mid-March, was later extended twice, with the latest extension being until 1 July 2020.