Yes, there are several female villains in the Teenage Mutant Ninja Turtles (TMNT) franchise. Here are a few notable ones:
1. Karai: After making a cameo appearance in Teenage Mutant Ninja Turtles in 1993, Karai made her first full debut two issues later in and went on to become a threatening member of the Foot Clan as Shredder’s second-in-command.
2. Alopex: Alopex is as peculiar a villain in the franchise as she is fearsome, as she proved in the 2012 animated series Teenage Mutant Ninja Turtles. She was originally introduced in the 2011 micro-comic series but has proved herself to be one of the most vicious villains ever since.
These characters add a unique dynamic to the TMNT universe and have been integral to many storylines throughout the franchise's history.