The fire started at 1:30 p.m. at the transit hub, which is still under construction.
The MTA says someone was welding on the roof and a spark touched some insulation, which caught on fire.
The Fire Department said they had some difficulty getting to the fire because of the location. It was placed under control just before 3:00 p.m.
There were no injuries reported.
The $1.4 billion transit center is scheduled to open next year. It's expected to serve 300,000 customers daily as it connects 6 different lower Manhattan subway stations.