An animatronic Bat-Mite briefly appeared in the "Deep Freeze" episode of Batman: The Animated Series, in which Bat-Mite enthusiastically greeted Batman, saying, "Greetings, Dynamic Duo! I'm your biggest fan!" before kissing Robin, who was shocked. It then malfunctions and falls apart, stuttering "I just wanna help!" as it does so. He was voiced by Pat Fraley. In the background, an animatronic Mister Mxyzptlk, Streaky the Supercat, and Krypto the Superdog can also be seen.
Bat-Mite appears in the episode "Legend of the Dark Mite!" trying to make Batman a better hero. Batman eventually manages to trick Bat-Mite into going away, but he later impersonates Ace the Bat-Hound and found out about the trickery. He then decides to turn Batman into his "toy" but Batman gives Bat-Mite a chance to become the actual Batman. But Bat-Mite's imagination grows wild, pitting him against many of the Batman rouges, including Two-Face, Killer Moth, and Catwoman. Batman saves him, and Bat-Mite apologizes to Batman. Batman tells him that he doesn't have to blindly follow his footsteps, and he can do anything he wants with his powers. After Green Arrow stops a robbery, a character similar to Bat-Mite in a Green Arrow costume, appears, proclaiming that he is his "biggest fan". He also appears in a later episode called "Emperor Joker!", where he goes to observe Batman's ultimate fight with the Joker. While they are fighting, Bat-Mite falls in love with the Joker's assistant Harley Quinn. When Batman was getting beat up by Joker and his henchmen, Bat-Mite tries to give his powers to Batman, but he misses and ends up giving his powers to the Joker. With his powers, Joker recreated the world in his image and killed Batman repetitively. Bat-Mite and Harley defeated the hencemen while Batman overcame the Joker until he was forced to give his powers back to Bat-Mite. After that, Harley said she wasn't interested in Bat-Mite because her true love was Joker. Both cartoons then end with Bat-Mite parodying Porky Pig's "That's all, folks" line.