The shooting happened near the San Ysidro crossing into Mexico, FOX 5 of San Diego and City News Service reported.
The man who was killed was described only as a non-U.S. citizen who became involved in an altercation with a border officer, the station reported.
The shooting occurred shortly before 6 p.m. local time near the Las Americas Premium Outlets mall, according to KFMB-TV of San Diego.
No further details were available from the Border Patrol. The incident remained under investigation.