Officers were alerted to the incident at St Aloysius' College, Hill Street, Glasgow, at about 21:00 on Sunday.
Inquiries into the graffiti are ongoing, police said.
St Aloysius' College said the graffiti on the Dalhousie Street side of the main building had been reported to police and removed.
A spokesperson for the college said: "Graffiti was discovered on the Dalhousie Street side of the main building on the morning of Monday, 22nd August, following the weekend.
"The matter was reported to police and inquiries are ongoing. The graffiti has now been removed."
A spokesman for Police Scotland said: "Around 2100 on Sunday, 21st of August, police received a report of vandalism at a school on Hill Street, Glasgow.
"The incident is being treated as a hate crime and inquiries are ongoing."
Police have said that sectarian graffiti which was daubed on a wall at a private Catholic school in Glasgow is "being treated as a hate crime".