K's Auto Repair, a Mineola auto body shop next to the LIRR tracks on Willis Avenue, went up in flames just before 11:30 p.m. Thursday.
Heavy flames shot through the one-story commercial structure, collapsing the roof of the business.
LIRR service on the Port Jefferson, Ronkonkoma and Oyster Bay branches was suspended because firefighters ran hose lines across the tracks. All were restored by 4:30 a.m.
No injuries were reported and firefighters expected to be pouring water on hot spots into the morning.
The cause of the fire is under investigation.