It happened at the restaurant on 13th and R Street just before 9 p.m.
Investigators say a man in his twenties pointed a gun at employees and demanded money from the safe.
The workers gave him cash, and the suspect got away before officers arrived.
This same location was robbed at gunpoint on Oct. 14.
Another McDonalds on Motel Drive in Merced was hit on Sept. 11.
The city has seen a spike in robberies this year.
The Merced Police Department had 156 cases by August, compared to 95 at the same time last year.