It happened around 5 a.m. near South Alston Avenue and East Pettigrew Street.
The man was taken to a hospital and later died from his injuries. On Tuesday afternoon, DPD identified him as Ronnie Earl Shaw, 42.
DPD said no passengers were on the Norfolk Southern train.
The crash remains under investigation.
East Pettigrew Street was closed at the intersections of South Driver Street, South Plum Street and Ramseur Street as officers investigated.