The flyers appear to have been distributed by the same group that's been targeting some Brampton neighbourhoods with an anti-immigration message.
The flyers show images of what they claim were students at York back in the 1960s, saying back then the student population was 100 per cent white.
Below that photo is a recent image of a more diverse group of students with text saying "soon whites will be the minority."
Mithilen Mathipalan is the student union's vice-president of equity and says he learned of the posters after students brought them to their office.
"The union is extremely appalled and disgusted by the flyers that are going around," he told CBC News. "Especially at a time like this in 2014. It's quite frankly pathetic that something of this calibre is going on in our communities."
York University says they sent an official notice to the group responsible telling them to remove the university logo and its photographs from their posters.
Police are investigating.