A Sydney private school student was indecently assaulted by a drunken boarding house supervisor who came to his room with a glass of wine late at night, a court has been told.

Mark Patrick Nelson, 26, has been charged with aggravated indecent assault over an alleged incident at the Shore private school in North Sydney on the night of June 24 last year towards the end of term two.

Giving evidence in the Downing Centre Local Court today, the alleged victim of the assault said Mr Nelson visited his room on a number of occasions while he and two friends were there.

He said Mr Nelson was in an emotional state and had been crying and saying that he was going to have to leave his boarding house role.

He said Mr Nelson had been touching his thigh on a number of occasions, which made him feel "extremely awkward".

Mr Nelson then allegedly "slid his hand up under the doona and pinched me hard where the leg meets the bottom".

"I pulled the doona up around my legs so he couldn't get under there," the young man said.

When the other students returned to their rooms, Mr Nelson allegedly stayed behind.

"He tried to get in the bed ... his chest was against my chest ... he rubbed his stubble against my arm ... it was way too close.

"I said 'What are you doing?' And he said 'Do you want me to go?' and I said 'Yes' and he got up and left."

Police claim that the assault was undertaken in "circumstances of aggravation", because the student was under Mr Nelson's authority as a school teacher and the assistant master of the boarding house.

An interim apprehended violence order has been taken out against Mr Nelson, preventing him from going near or contacting the alleged victim and a second youth, who is also a student at the school.

Mr Nelson has been stood down from his position at the school pending the outcome of the hearing.