Amtrak officials say the Carolinian train was running from New York to Charlotte when it hit the male just after 6 p.m. It happened on the tracks between Campus Drive, Swift Avenue, and Main and Pettigrew Streets.
Durham Police said the male was taken to Duke Hospital with a foot injury that did not appear to be life-threatening.
There were no injuries to the 328 passengers or crewmembers on the train.
The train was stopped for investigation, but was back on the move towards Charlotte around 7:30 p.m.