It happened around 3:30 am near Illinois and Diana Streets.
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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.
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Officials say drivers traveling downtown should expect some delays for at least another hour.