"We were engaged in good faith negotiations about my departure based on philosophical differences over the direction and future of Planned Parenthood."
The non-profit organization's board of directors said Wen was departing her role effective immediately and that former Planned Parenthood board chair Alexis McGill Johnson had been named acting president.
Planned Parenthood will begin looking for a new president and CEO early next year in hopes with the goal of having a permanent replacement by the end of the year, the group said.
Planned Parenthood tweeted that the rule was "not something that (the group is) going to participate in."
At least one state's Planned Parenthood office is opting not to accept Title X funds over the new rules.