The show revolves around a group of kids who are pirates in Neverland, looking for treasure. Their main obstacle is Captain Hook, his first mate Smee and Tick-Tock the Crocodile, Captain Hook's feared nemesis from Disney's Peter Pan franchise. Captain Hook usually sees Jake and his crew doing something fun and steals it from them, and Jake and his crew tries to get it back (They always succeed and Captain Hook is always the loser). Then Jake and crew count their Gold Doubloons (which they get after completing an obstacle) and continue having fun or do something else, like when they discovered the observatory. Then, it shows Captain Hook and Smee, and in some episodes, Smee give Captain Hook something, which usually backfires on him.
Each program contains two eleven minute animated episodes, followed by a live-action song by the Never Land Pirate Band. The singing characters "Bones" and "Sharkey" appear in both animated and live action forms.