There are some similarities. They are both episodic in nature (i.e., they unfold in a series of mini-"episodes" - like the magic shop scene and the dinosaur park in Pee Wee or the Laundromat and pet store in Fred). Both feature inexplicably man-childish (or teen-childish) main characters. They both have quest storylines.
However, Fred has far, far lower production values and not nearly the level of talent involved. I'm not a Fred-hater (my kids love Fred, and he's grown on me a bit), but Pee Wee is deservedly a classic.
From what I've seen from a couple of his videos that I didn't even watch all the way through, Fred does seem a bit like Pee-Wee Herman but with none of the wit.
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