The writers imagined a back story to connect this film to Pee-wee's Big Adventure (1985): Pee Wee had become famous, due to the "Pee Wee's Big Adventure" feature film (starring James Brolin and Morgan Fairchild), inspired by his adventure. Pee Wee had a lot of girls flock over him, when he became a Frank Sinatra-like singer. But, Pee Wee had found fame too much and decided to fly away and live a quiet normal life as a farmer in an old folks' community.
Due to Pee-wee's Big Adventure (1985) and this being produced by different studios (Warner Brothers for "Adventure," Paramount for this one), Danny Elfman's famous score for the earlier film could not be reused, so he had to compose a new score for this one.
For the movie's poster/VHS/DVD artwork; the body of Pee-Wee impersonator Jeff Scott was used; with Paul Reubens' head replacing Jeff's.
Tim Burton turned down the chance to direct, as he was transitioning from completing Beetlejuice (1988) to beginning pre-production on Batman (1989). He worked with Paul Reubens again on Batman Returns (1992) and The Nightmare Before Christmas (1993).