Gaspar Puch-Tzek, 22, had just gotten off work and was outside the restaurant at 19th and San Carlos streets when he was shot at about 12:30 a.m. on Aug. 30.
Puch-Tzek, who worked as a cook at Hogs & Rocks, and two acquaintances were standing outside the restaurant having a cigarette when two suspects approached and one shot him in the head, one of the restaurant's owners said.
He was taken to San Francisco General Hospital in critical condition and succumbed to his injuries that afternoon.
During their monthlong investigation, police received help from community members and local merchants, and developed enough information to arrest the teen, who was being held in San Francisco's Juvenile Justice Center on unrelated charges, police said.
He will now be charged with murder, firearms violations and a gang enhancement, according to police.
Police are withholding the teen's name because he is a juvenile.
At the time of the crime, police said Puch-Tzek might have been mistaken for a rival gang member, although he had no gang ties.