Police announced Ayame Stamoulis, 18, was taken into custody Thursday evening.
A maintenance worker discovered the body shortly before 6 a.m. on July 15 on the roof of the restaurant at 279 East 149th Street.
Police said the body was inside a plastic bag and wrapped in a moving blanket.
Police are investigating whether it was thrown from a higher building nearby.
The victim’s identity has not been released.
The cause of death is still under investigation.