Police say the men caught on surveillance video persuaded the guard to let them into the closed McDonald's on Varick Street in the West Village on around 4:30 a.m. Sunday.
Once the men were inside, they allegedly pulled out a gun, locked the guard in the bathroom and ordered the other workers to the ground.
Police say they made off with more than $2,000.
No injuries were reported.
Anyone with information in regards to this incident is asked to call Crime Stoppers at 1-800-577-TIPS (8477).