Harden, 61, is the third executive to announce a departure in recent months.
Longtime CEO Bill Corley said in June that he would retire at the end of next year.
Last month, Mark Dixon, who is in charge of the three Indianapolis hospitals in the Community system, resigned to take a hospital position in Minnesota.
Harden also oversees the system's behavior care service.
She will serve as president emeritus of Community East through 2009, the announcement said. In the new role, she will help the hospital with certain initiatives to strengthen the system's presence in the community.
Harden will be replaced on an interim basis by Steve Hultgren, network vice president of pharmacy.