It happened just before 11 a.m. Wednesday near Tuolumne and G Street.
Operators on the Union Pafific cargo train called police when the man was hit.
Investigators attempted CPR however he did not survive his injuries.
"There's a small homeless encampment out here. We believe he lived in this area in a tent. When he left where he was staying at tried to cross the tracks eastbound over here at G and Tuolumne. Struck and killed him," said Lt. Mark Hudson.
The man killed has not yet been identified - but he's described as hispanic and in his thirties.