It happened around 3:30 am near Illinois and Diana Streets.
Investigators say the man stood on the tracks while the train approached and as the conductor blared the horn.
The victim, a man in his 40s, died at the scene.
The train is stopped along the tracks, blocking several streets into downtown Fresno, including Tulare and Fresno Streets.
Officials say drivers traveling downtown should expect some delays for at least another hour.