The man has been taken to hospital. The extent of the injury is unclear, but he is said to have been conscious,
The police were alerted shortly before 11pm on Saturday evening by residents in the area who heard explosions.
Initially, the commuter train traffic was stopped and the subway turned around at Farsta centrum, but the traffic is running again.
The shooting is the second in a short time in the area. On July 14, a young man was shot dead in Farsta. A 17-18-year-old boy was arrested on suspicion of the murder, but was released.