The area opened in 1956, one year after Walt Disney opened the theme park. Two names considered for the island were "Mickey Mouse Island" and "Treasure Island." Ultimately, the Tom Sawyer theme was selected.

While the island has not seen tremendous change over the years, in 1992 the south area was renovated to accommodate the nighttime spectacular Fantasmic!. The $30 million dollar production has run many hundred times and is one of the most successful shows in Disneyland history, judging by guest popularity.

Disney has recently updated Tom Sawyer island with pirate elements for the premier of Pirates of the Caribbean: At Worlds End. Officially announced as a two-phase revamp into "Pirate's Lair at Tom Sawyer's Island" based upon stories in "Tom Sawyer" where Tom, Huck and Joe Harper pretend to be pirates on the Mississippi, this change would integrate pirate tie-ins with the original, but updated, Tom Sawyer feel.

Originally, the re-theming was thought to have been more drastic and specific to the movie. Some of the new additions include a stunt show on the Fantasmic stage, Pirate treasure salvaging, a meet and greet with Jack Sparrow, and a retheme of Injun Joe's Cave into Dead Man's Grotto, featuring a variety of special effects such as an animatronic pirate that switches between a normal and cursed form, a ghost guarding a treasure, the Dead Man's Chest complete with the feel of Davy Jones's heartbeat, and pop-ups of skeletal Pintel and Ragetti guarding a cursed treasure.

In addition to these, Fort Wilderness torn down after years of closure from termite damage and currently in its place is a new fort being built.