A Manhattan principal who was slapped on the wrist for having boy students stay overnight at his Brooklyn house has quietly stepped down.

John Pettinato, 61, retired as principal of the Institute for Collaborative Education in Gramercy.

His last day was Feb. 17, but he stayed on the payroll through July 1 because of unused sick days, officials said.

Pettinato was reprimanded last year after Schools Investigator Richard Condon found he was living with a student and an ex-student at his home in Bushwick, Brooklyn.