Claude Bernard Lyon 1 University confirmed the incident on Twitter shortly after 9.30 a.m., advising people to stay 100 metres away from the building.
It said explosions were the result of building work, and that three people suffered minor injuries.
Shortly after 10 a.m., the university said the fire was "under control" and that some buildings had been re-opened.
Police and university sources said the fire was started by a gas bottle explosion. Footage of the incident shared on social media showed the extent of the blaze.