Alternate versions

When the DVD was first released, it contained minor errors where a second of the Warner Bros. Family Entertainment logo and its fanfare are both removed, and the film's alternate title Free Willy 2 was used as the end title card. The two-disc version of the 4 Film Favorites Free Willy Collection retains the fanfare error and Free Willy 2 end title card, but also shortened the opening title card to Free Willy 2.

Some International printings tweaked the audio pitch.

The end credits is the only scene in the VHS release to be presented in widescreen which happens to be the film's actual format. All the other scenes were presented in pan and scan.

The 2000 airing on NBC made several tweaks including some scenes that were shortened. The only full scenes this version cut are Jesse getting caught by Elvis for aiming the flashlight at him while he's asleep, and Randolph testing the skookum on Jesse. In addition, a clip of the Dakar's first appearance plastered Joan Lunden presumably due to Good Morning America, which airs on ABC, being a network rival to NBC's Today show. Lunden's voice can still be heard when John and his assistant briefly watch her report on the TV screen.

A version on the digital platforms, and post-2022 airings on HBO Family is identical to the International version due to the opening and end title cards both being titled Free Willy 2.

1-800-4-WHALES phone number does not appear in the end credits to the 2000 NBC airing nor post-2003 prints