Pee-wee Herman (Paul Reubens) has a dream of being a famous singer. He makes his exit by disguising himself as Abraham Lincoln. One of the fans asks him for his autograph, but his disguise is promptly exposed. They chase after him and he flies off to his ranch. Pee-wee finally awakens from his dream that morning to work on his farm with Vance the pig (voiced by Wayne White). Later, he has lunch with his fiancée, school teacher Winnie Johnson (Penelope Ann Miller). Next, he races Vance to a general store owned by Mr. Ryan (Albert Henderson) to order a cheese sandwich with a pickle.
The sheriff (Kenneth Tolby) warns everyone of a big storm approaching town. After the storm ends, Pee-wee emerges from his storm shelter to discover that an entire travelling circus has been blown into his backyard. Befriended by Cabrini Circus manager Mace Montana (Kris Kristofferson), Pee-wee is hoping to impress Gina Piccolapupula (Valeria Golino), a trapeze artist and the circus' star attraction, thereby incurring the jealousy of his Winnie until she meets Gina's older brothers: The Piccolapupula Brothers. Gina leaves Pee-wee when she finds out about Winnie, but later returns to him when she realizes that Pee-wee actually loves her.
Pee-wee wants to join the circus, but his attempts fail. Gina then tells Pee-wee about her deceased father, Papa Piccolapupula, who was a famous aerialist who suffered a fall performing the Spiral of Death, and that Pee-wee should try walking the tightrope in his honor.
Mace comes up with a brilliant idea: to stage a three-ring spectacular saluting the American Farm. The problem is that the majority of the town's residents are disgruntled, uncaring elderly people who have been demanding the circus Pee-wee is helping leave town. The townspeople attempt to arrest Pee-wee for various crimes including defacing public property. The sheriff agrees to drop the charges however provided that the circus leaves town. The circus does so, but Pee-wee saves the day when he sneaks genetically modified cocktail weenies from his hot-dog tree to the townspeople, causing them to become children once again. Now grateful to have extra years of life and without any memories of what happened, the children watch Mace's circus and Pee-wee perform.
- Paul Reubens as Pee-wee Herman: An eccentric, childish farmer and scientist living on the outskirts of a small rural town.
- Kris Kristofferson as Mace Montana: the owner and operator of the Cabrini Circus that is blown onto Pee-wee's farm by a huge storm.
- Susan Tyrell as Midge Montana: Mace's extremely small wife, who often leads the members of the circus when her husband is not around.
- Valeria Golino as Gina Piccolapupula: A trapeze artist in Montana's circus with whom Pee-wee falls in love.
- Penelope Ann Miller as Winnie Johnson: A school teacher and Pee-wee's former fiancée.
- Albert Henderson as Mr. Ryan
- Wayne White as the voice of Vance the Pig: Pee-Wee's talking pig.