The accident happened at Jeanne and Fountain Way - just before four o'clock Wednesday afternoon.
Investigators aren't sure why the man and a woman were walking along the tracks, or why they didn't get out of the way.
Police say the freight train was traveling about 60 miles an hour at the time.
The woman died after being struck by the train, and the man was taken to Community Regional Medical Center.
Lt. Mike Doyle said, "This has happened before where individuals walking on the train do get caught in a narrow area and think there's clearance but there is equipment from the train that does stick out, it probably took them by surprise."
The accident caused rail traffic through Fresno to back up for several hours.
Two Amtrak trains also experienced delays, and passengers on one train were stuck on the tracks for nearly an hour and a half.