Not many anime have female leads, here is a list of the ones that I know about. This will also include anime, where there are multiple protagonists.
If you know of one, that is not listed, please...
Every single of my plan to watch anime is in this list alphabetically.
Anything with a run time of less than 20 minutes, and has 3 or more episodes is on this list. Including DVD/TV specials for longer run-time shows. The list is ordered with stand alone shows first...
A list of anime I've seen with a main cast of only female characters. I was bored. No sequels added.
Short comments for all the anime I've watched. A constant work in progress.