A depraved Brooklyn school aide was arraigned Saturday on charges that he sexually assaulted a 9-year-old girl multiple times inside the school where he works.

Special education paraprofessional Kevin Lemon, 28, allegedly sexually abused the student in the basement and a staircase at PS 59 in Bedford-Stuyvesant on at least three occasions in June, prosecutors said in Brooklyn criminal court.

The victim, who is not a special-needs student, suffered the abuse through the end of the school year in June, officials said.

When the student saw him again at the start of school in September, she told her great-grandmother — who is her legal guardian — what Lemon had allegedly done, and the two reported the educator to police.

The courtroom audience gasped as prosecutors detailed the three alleged incidents.

Lemon was arrested Friday night in Brooklyn and hit with a slew of charges, including criminal sex act, sex abuse, forcible touching, sexual misconduct and endangering the welfare of a child.

The staffer, who earns $158 a day, according to public records, was led out of the NYPD’s Special Victims Unit detention building shortly after his arrest, wearing a gray jacket with his hands cuffed behind his back.

He did not comment to reporters.

“These are deeply disturbing allegations and we immediately suspended this substitute paraprofessional without pay,” a Department of Education spokeswoman told The Post.

“He will remain suspended without pay pending the outcome of the investigation,” a Department of Education spokeswoman told The Post.

Lemon was ordered held on $50,000 bail and is due back in court Thursday.

His lawyer, Aminie Woolworth, said Lemon has strong ties to the community. He said he is studying to be a teacher at Brooklyn College and is just six credits shy of graduating.

Woolworth said there were “many issues” in the case, and the girl “does have some issues.”

Lemon is the second city employee to be arrested this week for sexually abusing a minor. On Friday, NYPD Special Victims Det. Juan Jimenez, 37, was busted for allegedly groping and attempting to kiss a 12-year-old girl in Brooklyn.