The Knocked Up producer set the project in motion after seeing Reubens' zany revival of the Pee-wee Herman Show, which ran in Los Angeles from January to February (10).
The show was a revamp of Reubens' 1981 stage production that landed the actor and his beloved character a TV show and a film franchise.
Paul Rust, whose credits include Inglourious Basterds and I Love You, Beth Cooper, will reportedly pen the new screenplay, which will take Pee-wee on "a gigantic adventure".
Apatow tells Daily Variety, "Let's face it, the world needs more Pee-wee Herman. I am so excited to be working with Paul Reubens - who is an extraordinary and ground-breaking actor and writer. It's so great to watch him return with such relevance."
The movie deal follows Reubens' announcement he will take his smash stage revival to Broadway, for a six-week New York run in November (10).
The actor previously took the character to the big screen with Pee-wee's Big Adventure in 1985 and Big Top Pee-wee in 1988.
He retired the character in 1990 after 13 episodes of Emmy Award-winning children's TV series Pee-Wee's Playhouse.