Alternate versions

In August 6, 2002, the Director's Edition was released on DVD, which features three minutes of footage not in the theatrical release: (The Director's Edition does not use the ABC-TV version of Kirk and Saavik's conversation in the turbolift, which was more steamy and used close-ups (instead of one long master shot). Also, unlike the ABC-TV version, all Ceti eel scenes are not edited for content.

• Expanded conversation between Kirk and McCoy in Kirk's apartment about his birthday gift, the glasses. Also, McCoy now says "For most patients your age, I'd usually administer Retinax Five." This is an alternate take, since in the theatrical version, he says "recommend" instead of "administer" (Seen in ABC-TV version).
• Conversation between Kirk and Midshipman Preston in the Enterprise's engine room, with Scotty revealing that Preston is his nephew. Also, the take at the scene's ending with Kirk addressing Scotty and McCoy asking "Admiral, what about the rest of the inspection?" is different from the one seen in the theatrical version. Kirk's dialogue is also slightly different (Seen in ABC-TV version).
• The scene where Chekov informs Dr. Marcus and her team about their new orders via compic has been expanded. Carol Marcus now asks "Who gave the order", and the mind controlled Chekov dances around the answer a little before David says, "Pin him down, mother." (Seen in ABC-TV version).
• The scene where the scientists at Regula One argue about Starfleet Command's order is a different take, and has been expanded in the ending to show Carol Marcus ordering everyone to pack their things up so they can depart before the Reliant arrives (Seen in ABC-TV version).
• McCoy and Spock's argument about Genesis in Kirk's cabin has been slightly expanded. They discuss what might happen if Genesis fell into the wrong hands, and whose hands are the right ones. Kirk attempts to break the two up, but Spock cuts him off with a comeback to McCoy (Seen in ABC-TV version).
• Preston's death in Sickbay has been expanded. Preston now says "Aye" and dies in close-up (instead of in the medium shot with Preston's back to the camera and the others visible around the table seen in the theatrical version) Scotty asks why Khan wants revenge. McCoy's line, "I'm sorry, Scotty" now comes in the middle of the scene, instead of in the ending. After Spock informs Kirk via intercom that impulse power is restored, McCoy and Kirk speak a little longer, and Kirk says they only survived because he knew something Khan didn't about starships (Seen in ABC-TV version).
• An added shot of Kirk, Spock and Saavik climbing a ladder between decks has been added, in which Kirk says "That young man, he's my son," and Spock replies, "Fascinating." Also, the music in the scene has been looped to account for this added shot, but it loops at an earlier point than in the ABC-TV version. This makes the music flow better, instead of repeating the same bit of music twice in succession. For the 2016 Director's Cut Blu-Ray edition, the shot is included but the dialogue is omitted.
• An extension occurs as the Enterprise approaches the Mutara Nebula. Saavik wonders if the Reliant will follow them in, and Spock states that he must remember to teach her about the human ego. The music is looped at a different point than in the ABC-TV version to accommodate this extension, and it is thus much less distracting.

The UK cinema and original video version was deleted by around six seconds and released as PG. Only later was the video reissued uncut as a 15 Cert. The scene deleted from was a closeup shot of the 'bug' coming out of Chekov's ear.

Additional dialogue featuring David Marcus and Saavik was shot for the film's epilogue on the bridge, but this was deleted.

Original film prints did not include the "II" in the title.

All versions shown on the Sci-Fi Channel, TBS and TNT, and syndicated television versions are reedited versions of the theatrical version, and not of the ABC-TV version.

The Kobayashi Maru simulator computer has more dialogue in the ABC version.

In the network television version, during the sickbay scene where the young ensign dies, we find out that the ensign is actually Scotty's nephew, thus explaining Scotty's emotional state. In a version that aired on AMC, the relationship between Scotty and the ensign is established in a scene where Kirk is inspecting the Engineering section. He and the ensign have a spirited discussion, afterwards Scotty mentions in a light-hearted asside to Kirk that the ensign is his sister's youngest son. In the theatrical version, the same scene is shorter, leaving out any mention of who the ensign is and why Scotty is so upset.

The Director's Edition also has a different font for the subtitles when Spock and Saavik have their Vulcan exchange in the torpedo bay.