A man pistol-whipped and shot a straphanger in the thigh during a robbery on board a Queens shuttle train over the weekend, police said.

The 36-year-old victim was riding a Far Rockaway shuttle after transferring from a southbound A train at around 9 p.m. Sunday when a stranger walked up to him brandishing a gun, police said.

Cops said the armed man smashed the victim in the head with the firearm while demanding that he hand over his valuables.

The subway rider complied and gave the attacker his wallet, which police said contained about $120 in cash, and his identification cards.

Despite getting hold of the loot, police said the armed mugger opened fire on the victim, striking him in the upper thigh.

The suspect then got off the shuttle train at the Rockaway Park-Beach 116 Street station and fled on foot.

Paramedics arrived at the station and transported the shooting victim to Brookdale Hospital Medical Center in stable condition.  

The shooter was last seen on a security video wearing a black ski mask covering most of his face and a pair of blue gloves.