The 18-year-old clerk, whose name was not released, was inside the station at 63 Eighth Ave., near 13th Street, about 2 a.m., when a man swiped a pack of cigarettes and bolted for the door, the NYPD said.
The teen ran after him, but the shoplifter turned around and stabbed his left hand with a knife, police said.
The clerk had to get stitches at Bellevue Hospital, the NYPD said.
Vas Hondros, 25, who manages the station, said the teen is OK and will be back at work tonight. He said it's the first time anything like this has happened at the family-owned gas station.
"I never encountered any problems here before like that," Hondros said.
But Hondros said he's heard about other crime in the tony neighborhood.
"A couple people told me there's been break-ins at stores around here," Hondros said. "It's a good neighborhood, but I wouldn't consider it safe, you know?"
The suspect, who was wearing a bulky hooded jacket, is believed to be 35 years old, about 200 pounds and 5-foot-10, police said.
Hondros said his father, who owns the gas station, recognized the man from surveillance footage as someone who has come into the store before.
Hondros said he's ready if the man returns.
"If he comes back, I ain't gonna let him go," he said.
Anyone with information is asked to call Crime Stoppers at (800) 577-TIPS (8477).