Peterborough Lakefield Community Police say the woman told them she was alone in a classroom at about 3:10 p.m. Wednesday with the boy when she was attacked.
Police allege the boy came up behind her, choked her and sexually assaulted her by trying to take off some of her clothing.
Neither police nor the school board will identify the school, but the board says the woman is a child and youth worker.
The 13-year-old was arrested at school soon after and was charged with sexual assault and overcoming resistance to commit an indictable offence, in relation to the alleged choking.
The boy, who can't be identified under the Youth Criminal Justice Act, was held in custody overnight and is set to appear in court today.
Peter Mangold, the superintendent of education at the Kawartha Pine Ridge District School Board, said the staff member is doing all right, considering the circumstances.
"In a volatile situation you can't always anticipate the actions of every student," he said. "Fortunately she's OK, but it certainly is something that we're really, really concerned about."
CORRECTION: This is a corrected story. A previous version identified the alleged victim as a teacher.