There is a scene in the movie where Reno (Pepe Serna) and New Jersey (Jeff Goldblum) go through a room with a watermelon in a machine really out of place for the scene. Reno says "I'll explain it later". In the Blu-ray audio commentary, filmmakers explain that they had a "confrontational" relationship with one of the producers. When they stopped receiving notes from the production, they decided to put the watermelon in a scene with no mention about it anywhere on the script. When they received no questions about it, they deduced that no one was screening the dailies anymore and they could keep making the film the way they wanted to as long as they remained within the budget.
Jamie Lee Curtis played Buckaroo's mother in a flashback, but this scene was deleted. The scene is available on the recent DVD release as an optional prequel to the theatrical version, and as a special feature. Jamie Lee Curtis is visible in a photo on the dashboard of the jet car in the wide-screen version.
According to Peter Weller, he had a particularly tough time filming the scene without laughing where Lord John Whorfin (Dr. Lizardo) is torturing Buckaroo with electricity, because it was the first time he had heard John Lithgow perform what Weller likes to refer to as John's "Italian/Martian accent".
The movie's ending invites the viewer to watch for the upcoming film "Buckaroo Banzai vs. The World Crime League". This was the title for a sequel that Sherwood Studios planned to make, if this film had been successful. Unfortunately, it was a box-office bomb, and Sherwood Studios went bankrupt. However, after its release on video and cable, the film became a cult favorite, much in the same way as Mad Max (1979) (which crawled from obscurity to spawn two sequels). Legal wrangling, due to the bankruptcy, prevented any other studios from picking up the sequel rights, and even many years later, MGM had to fight through a pile of red tape simply to get the OK to re-release it onto home video (DVD). In 2021, the novel "Buckaroo Banzai Against the World Crime League" was finally released.
In the original script, Buckaroo was supposed to have an archenemy named Hanoi Xan, who was never seen, but referenced to by Buckaroo and the other characters. All scenes containing dialogue regarding Xan were deleted from the film's theatrical release, but are now available on DVD. Xan was supposed to be the mysterious head of a crime syndicate called the World Crime League, and also the man who murdered Buckaroo's parents and wife Peggy.