Police closed the station for about half an hour to investigate.
Investigators say the incident started at about 1 p.m. on a train headed to Daly City.
Witnesses say two men aboard the train started arguing and the argument escalated as the train reached West Oakland.
"The train approached the station. They got into a physical altercation. That's when a firearm was produced. Someone was hit in the head with it. The shot rang off," said Ivan Rodriguez who was on the train. "Can't really tell you what happened after that cause as soon as that happened we hit the floor."
The gunman was gone by the time BART police arrived on scene.
Witnesses also say the shooting victim was only grazed by the gunfire.
He was taken to a hospital, but is expected to recover.
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