Police say it happened just before 10:00 p.m. Saturday near Ninth and South E streets.
Officials say they received a call from Union Pacific Railroad, saying a northbound train hit a man.
When officers arrived, they found a 39-year-old man lying near the tracks and provided medical aid.
He suffered significant injuries and died on the way to the hospital.
The man has not been identified and why he was on the tracks is unknown.