The fire broke out at 6 East 43rd Street between Fifth and Madison avenues, an alarming sight for the crowds gathered for the celebration.
The wind-driven fire was under control within about an hour and a half and authorities said there was no impact to the parade.
Authorities say a cooling tower on the roof caught fire a little before 10 a.m.
"It was a wind-driven event, the units took about 140 fire and EMS personnel on scene to take care of the situation," FDNY Deputy Chief Brian Whiston said.
The fire department said the 28-story building is being renovated into apartments. The only people inside were construction workers who all managed to evacuate safely.
Officials said an EMS lieutenant and a police officer suffered minor injuries.
Those at the parade said they were thankful that the fire wasn't more serious.
"This is the 25th anniversary of 9/11, and many of us have been thinking about how special the FDNY are for this parade, for life in our city and for protecting us, and so we're just reminded how fragile life is," one parade-goer told Eyewitness News.
The exact cause of the fire is not yet known.
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