A teacher’s assistant at Bay Shore High School pleaded not guilty Friday to charges that he raped a student from the school.

Marcus Johnson, 27, of Bay Shore, was ordered held on bail of $40,000 cash or $80,000 bond at his arraignment in First District Court in Central lslip. The district attorney’s office had asked for bail of $100,000.

A prosecutor told the judge that Johnson raped the victim twice, when the student was 14 and 15.

Judge Jennifer Henry issued an order of protection barring Johnson from any contact with the victim. Henry called the charges “very serious.”

The suspect is due back in court Oct. 4. His defense attorney, William Lavelle of Patchogue, declined to comment.

Johnson works with autistic children, but the victim is not one of them, police said earlier.

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Johnson used compliments to lure the girl into his home, Suffolk County police said.

School officials notified police, who arrested him Thursday night at his other part-time job, as a clerk at the Finish Line sports store in the Westfield South Shore mall in Bay Shore, authorities said.

He was charged with second-degree rape, third-degree rape and two counts of endangering the welfare of a child.

The school district did not respond Friday to questions about Johnson’s status at the school.

The district issued a statement saying that it “became aware of an allegation involving an improper relationship occurring outside of school between a female high school student and a male paraprofessional.

“The matter was promptly investigated by school officials and referred to the Suffolk County Police Department, resulting in an arrest,” the statement said.

“The safety of our students is always our paramount concern. We will continue to cooperate with the police department on this matter,” the statement concluded.

Detectives from the special victims section want to know if there are other allegations against Johnson and ask anyone with information to call them at 631-852-6531.

CORRECTION: A previous version of this story included an incorrect photograph of the suspect.