A man with a lengthy rap sheet has been charged with raping an 11-year-old Brooklyn girl three times, cops and prosecutors said Sunday.

Andre Clarke, 45, of Staten Island, most recently assaulted the child in her Brownsville apartment at around 9 a.m. Saturday, police allege.

She was taken to a hospital in stable condition.

Clarke, who was captured in Queens, had raped the victim two other times since Dec. 28, prosecutors said at his Brooklyn Criminal Court arraignment.

He was charged with three counts of rape in the first degree and ordered held in lieu of $250,000 bail.

Clarke used to be in a relationship with the victim’s mother and carried out his latest attack at his ex’s home, prosecutors alleged.

On Saturday, prosecutors said, Clarke was caught by the mother standing naked in the victim’s bedroom.

He fled the home, but a day later called a detective and turned himself in, prosecutors said.

Clarke’s ex-girlfriend has filed several orders of protection against him dating to 2016, according to police sources.

Four of his 11 arrests involve alleged domestic violence that occurred at that address, the sources said.

Clarke’s other arrests have been for robbery, menacing, harassment, DWI and assault, they said.

Police are looking into whether Clarke has victimized other children.