The show centered on a shipwrecked boy named Jimmy. Jimmy and his friend, a talking flute named Freddy, take a ride on a mysterious boat, which promised adventures across the sea, to kooky Living Island, home of dancing, talking trees and singing frogs. The Mayor of Living Island was a friendly and helpful dragon named H.R. Pufnstuf. The boat was actually owned and controlled by a wicked witch named Wilhelmina W. Witchiepoo who rode on a broomstick-like vehicle called the Vroom Broom. She used the boat to lure Jimmy and Freddy to her castle on Living Island, where she was going to take Jimmy prisoner and steal Freddy. But Pufnstuf found out about her plot and was able to rescue Jimmy when he leaped out of the enchanted boat with Freddy and swam ashore.
Jimmy was taken in by Pufnstuf, who was able to protect him from Witchiepoo, as the cave where he lived was the only place her magic had no effect. Apart from Jimmy and Witchiepoo, all of the characters on Living Island were realized via large cumbersome costumes or puppetry. Since everything on Living Island was alive, virtually any part of the Living Island sets could become a character. A frequent plot device involves Witchiepoo and her henchmen Orson Vulture, Seymour Spider, and Stupid Bat trying to steal Freddy only to be thwarted by Pufnstuf. Another concerns Jimmy and Freddy's efforts to return home from Living Island with the same lack of success.