The incident happened inside the Wien Far Kitchen on Church Avenue just after 11:30 p.m. Monday.
Police say at least six shots were fired and two 20-year-old men were struck. One was shot in the back and pronounced dead. The second was shot in the leg and rushed to Kings County Hospital in stable condition.
A restaurant worker was hit when the bullets shattered the bullet resistant glass at the counter, sending shrapnel flying into his torso. The worker was also in stable condition.
Two gunmen fled the scene, and no arrests were immediately made.
Authorities are investigating the circumstances of the shooting.
