Camille Cates Barnett announced her decision in a tearful news conference at City Hall on Wednesday. The resignation is effective June 30.
Barnett is second in command to Mayor Michael Nutter.
She says she needs time away from the public spotlight to rebuild her personal life after the death of her husband, who was killed in a car accident days before Nutter's inauguration in January 2008.
Barnett has been credited with helping to set up the city's 311 non-emergency call system and creating a system to monitor the performance of city departments. But she also clashed with some members of the administration.
Nutter's office says there has been no decision on her replacement.
