My Gym Partner's a Monkey has been referenced by a currently less-than-sizable amount of TV shows. Most of the shows that reference to it have either been other Cartoon Network crossover episodes, or other works by Tim Cahill and Julie McNally.
- The Grim Adventures of The Kids Next Door, crossed over The Grim Adventures of Billy & Mandy and Codename: Kids Next Door. They had cameos of several other Cartoon Network shows, and came out at the perfect time, (during the final year of what most fans consider the network's "City Era") At this time, almost all of CN's programming consisted of unforgettable classics, which at the time, were either in the height of their popularity, or nearing their series finales. The two greatest shows at the time, were chosen for a half-hour crossover episode, but that didn't mean, they wouldn't be making shout outs to all of the other greats. One of those was My Gym Partner's a Monkey, which was referenced to a handful of times here.
- When Mandy was trying to get Numbuh 1 to him talk, she turned on the TV to show Fred Fred Burger, who would torture him with his obnoxious rambling. Fred Fred Burger described his favorite TV shows. One of the kinds of shows he like was about monkeys who go to school.
- When The Delightful Reaper was taken out, a countless amount of children from other shows were seen, flying out of it, as it exploded. One of which was Adam Lyon.
- During the ending credits, there were a series of faux promotional images for crossovers between other Cartoon Network shows. One of which crossed over My Gym Partner's a Monkey and Dexter's Laboratory to make a special called "My Gym Partner's a Mandark". The promotional image depicted Mandark Astronomonov swinging around the Charles Darwin Middle School on Jake Spidermonkey's tail, putting the latter in a great deal of pain.
- In the Billy and Mandy episode, "Billy and Mandy Moon the Moon", which was part of yet another city era crossover, Cartoon Network Invaded, they made callbacks to the previous shows note in the crossover, during the ending credits. In the credits, aliens abducted a character from each show and sucked their brains out. Sadly though, all these characters were the unintelligent buffoons of their respective shows and from My Gym Partner's a Monkey, their chosen character was the empty-headed Slips Python.
- In the O.K. K.O.: Let's Be Heroes! episode, "Crossover Nexus", heroes from other Cartoon Network shows were being taken from their respective worlds and thrown into the O.K. K.O. universe, where they would be frozen to stone by Strike. There was a prison, where all of Strike's previous victims were discarded, after he was done with them, creating an entire warehouse full of easter eggs from other shows. One of these characters was Jake Spidermonkey from My Gym Partner's a Monkey.
- In an episode of Littlest Petshop titled "It's the Pet Fest - Part 1", a talent agent talks to the main character about a bunch of animal themed bands. All of them are just generic animal band names, except for "Adam and The Spidermonkeys". This is obviously a Gym Partner reference, as both shows were created by the same people.
- In the Robot Chicken episode, "Boo Cocky", a guy was looking at a bunch of parody shows on his DVR. One of the parody titles was "My Gym Partner's a Vampire".