Paul Reubens was originally supposed to voice Flapjack. He never showed up on the day of voice recording, so series creator Thurop Van Orman decided to do it himself.
Thurop Van Orman originally wanted to continue the show past the 3rd season and was even considered of making a TV movie, but decisions in programming changes by executives from Cartoon Network and most of the show's crew wanting to move on working on then forthcoming shows Adventure Time and Regular Show caused Orman's plans for the shows's future to be canceled.
Captain Knuckles was based off an old fisherman Thurop Van Orman met when he was a child who gave him candy and told him stories.
Show creator Thurop Van Orman originally came up with the idea for the show in 2001 and pitched the show to Cartoon Network that same year and again in 2004 before it was picked up in 2007.