Michael Bay and Jerry Bruckheimer initially wanted a budget of $208 million, which caused conflict with Walt Disney Studios executives; the budget was eventually reduced to $140 million.

To help meet the reduced budget, many crew members—including the director of photography, editor, production designer, and lighting director—agreed to defer $5 to $10 million in pay, and companies like Panavision, Technicolor, and Industrial Light & Magic also agreed to deferrals; Michael Bay deferred his own salary as well.

Michael Bay wanted to make an R-rated film depicting the horrors of war graphically, but Disney ordered a PG-13 cut; as a compromise, Bay was later allowed to release an R-rated Director's Cut on DVD in 2002.

Michael Fassbender auditioned for the role of Rafe and received a rejection note from Disney describing it as 'really nice.'

Matt Damon was initially set to play Danny Walker but dropped out to star in Ocean's Eleven instead.

Charlize Theron turned down the role of Evelyn to star in Sweet November, and Neve Campbell auditioned and was offered a part but had to decline due to scheduling conflicts.

A set at Rosarito Beach in Baja California, previously used for Titanic (1997), was reused to recreate the sinking battleships during the Pearl Harbor attack, including a large-scale model of the bow of USS Oklahoma mounted on the world's largest gimbal to simulate the ship rolling and submerging.

The museum ship USS Lexington in Corpus Christi, Texas, stood in for both USS Hornet and a Japanese carrier, with its on-display aircraft removed and replaced by film aircraft and WWII-style anti-aircraft turrets for all the takeoff scenes.

Additional filming took place aboard USS Hornet, USS Constellation, and the museum battleship USS Texas near Houston, and many active-duty military members and local Hawaiians served as extras.

The Naval Historical Center advised the production against depicting Jimmy Doolittle as 'a boorish, oafish guy,' and this recommendation was accepted for the final portrayal.

Disney held the film's premiere aboard the active nuclear aircraft carrier USS John C. Stennis, which sailed six days from San Diego to Pearl Harbor to host over 2,000 guests on a specially built outdoor theater on the flight deck, at an estimated cost of $5 million.

Pearl Harbor became the first Worst Picture-nominated film (at the Golden Raspberry Awards) to also win an Academy Award, taking home the Oscar for Best Sound Editing, and it remains the only film directed by Michael Bay to win an Academy Award.

Many Pearl Harbor attack survivors and figures like Kenneth Taylor criticized the film's historical accuracy, with Taylor calling it 'a piece of trash... over-sensationalized and distorted'; producer Jerry Bruckheimer acknowledged, 'We tried to be accurate, but it's certainly not meant to be a history lesson.'

The film's score was composed by Hans Zimmer and was nominated for the Golden Globe Award for Best Original Score, while the song 'There You'll Be' received Academy Award and Golden Globe nominations for Best Original Song.