David Mark Street, 55, is facing one charge of theft under $5,000.
Street just took the job at the Vancouver Island high school last fall, but according to court documents he allegedly started taking money shortly after he arrived.
The court documents don't specify how much cash may have gone missing, but said the alleged theft occurred between mid-November and the end of March.
Nanaimo-Ladysmith School District Superintendent John Blain said the district is "deeply troubled by the allegations."
Street is no longer working for the district and was not paid severance, Blain confirmed.
Meanwhile Street's name has also been removed from the school's website and replaced with the vice-principal's, who has been moved up to take over the job
The allegations against Street haven't been proven in court. He is scheduled to make his first court appearance June 16.