Michael Resnick is the city's former public safety director and a longtime government official.
He will replace Blanche Carney, who retired last Friday.
The prisons have been plagued with problems from escapes to homicides and a years-long staffing crisis.
The mayor's office said Resnick has spent over two decades working in a variety of public safety and criminal justice system positions for the City of Philadelphia and the State of Maryland.
In 2016, he served as Acting Philadelphia Prisons Commissioner, including during a period when the City received a MacArthur Foundation grant to implement reforms to ease prison overcrowding.
Resnick also served the State of Maryland as Commissioner of Pretrial Detention and Services in the state's Department of Public Safety and Correctional Services, where he was responsible for overseeing the Baltimore City jails.