York Regional Police say the graffiti, which included the words "Fuck Israel," appeared on the bus shelter between midnight and 7 a.m.
Police described the bus shelter as being in the Bathurst Street and Clark Avenue West area.
Ethan Eisen saw the graffiti himself and posted a photo of it on Twitter. He told CBC News that the bus shelter is located at Atkinson Avenue and Spring Gate Boulevard.
The incident is under investigation. Police say they will review any available video from the area, or from buses that were passing through.