Investigators say the suspect fired off 12 rounds at the smoke shop on Highway 6 at Bellaire Boulevard just before 9 p.m.
He was among a group of seven robbers who were seen on surveillance cameras rushing into the shop.
No customers were inside the store when the incident happened, officials said.
ABC13 was told the employee who was hit was shot one time in the abdomen and was rushed to emergency surgery.
Investigators are reviewing surveillance footage to identify the suspects, but the men were in and out of the shop within just five seconds. They believe all but one of the men wore masks. Another possible clue investigators are looking into is the fact that one of the suspects dropped some merchandise in the parking lot.
Investigators are also working to learn whether the suspects could be responsible for similar crimes that have happened in the area.