Fans filmed the unbelievable moment he walked around the pitch with the weapon in his hand.
The incident occurred during an amateur match in the western Honduran town of La Jigua.
According to local reports, the referee whose name wasn’t given, brandished the pistol to protect himself from angry supporters who thought he should have awarded their side a penalty.
Shots could be heard in a video which went viral, although it was unclear where who fired the shots.
One supporter hurled insults at the ref by calling him a son of a b****.
There were no reports of any injuries as a result of the standoff.