His resignation will become effective on Aug. 30.
"I can't afford to continue this battle, even though I know, if given due process, I would be vindicated," Filner said, defiantly.
Filner has been accused of sexual harassment by at least 18 women, many of whom are still active in the city's political scene. That includes his former communications director, who is now represented by celebrity lawyer Gloria Allred in a lawsuit against Filner and the city.
He attempted to save his job as mayor by undergoing an intensive therapy for two weeks.