Police are accusing an after-school aide at Angelo Patri Middle School of raping a 13-year-old girl after luring her to his Highbridge home on Dec. 4.

Police arrested Michael Jenkins, 24, Thursday morning. He faces charges that include rape, criminal sex acts, forcible touching, sex abuse and acting in a manner injurious to a child.

The girl told someone at the school about the incident, and then it was reported to the NYPD's Special Victims Crime Unit.

Jenkins was a group leader in a SONYC after-school program for middle school students, but he was not a Department of Education employee.

He had passed state and city background checks prior to his employment.

"The safety of young people is our top priority, and we take allegations of this nature very seriously," the program's overseer said in a statement. "The individual was immediately suspended without pay, and he is no longer permitted in any schools."