Police released video that they say shows 28-year-old Ezekiel Dunn running on East 117th Street away from the restaurant.
Police say Dunn began harassing and arguing with employees inside the restaurant at 3rd Avenue and East 117th Street at around 12:30 a.m. Wednesday.
It is believed he had trouble ordering food from a kiosk and went to the counter to speak with a female manager when they started to argue.
The 31-year-old victim, who works in the kitchen, came out with a broom handle or stick in hand to defend the staff and was stabbed multiple times, including three times in the back, once in the arm and twice in his left temple with a box cutter.
He was rushed to Harlem Hospital and was being treated for injuries including a collapsed lung, but it appears he is expected to survive.
The incident marks the second time this year that an overnight fast food worker was assaulted. In January, Burger King employee Kristal Bayron-Nieves was shot and killed just around the corner.