Though Karen Gillan was unaware of a female Joker, there could very well be a female version of the Clown Prince of Crime in the upcoming Flashpoint movie.
Karen Gillan appeared at the Florida SuperCon over the weekend, where she said she wants to play The Joker in a future DCEU movie if given the chance.
Karen Gillan would make an interesting choice to play The Joker, but at this time it is not clear if Lauren Cohan will reprise her role or if that part of the Flashpoint story will even be touched upon.
But there is a precedent already set, which may play out in the upcoming Flashpoint movie.