The incident happened at the Prospect Park station on Flatbush Avenue and Lincoln Road just after 5 a.m.
Police say several men banged on the booth and ordered the clerk to open the door. When she would not, they poured a flammable liquid around the booth and lit it on fire.
They then fled.
The clerk, who was not seriously injured, was able put out the flames with a fire extinguisher.
She was taken to Methodist Hospital and treated for smoke inhalation. She was also being treated for trauma.
The station serves the B and Q lines. Service was not affected.
