The tusker was feeding on the foliage of trees close to the tracks when the mishap occurred between Raiwala and Motichur, Rajaji Tiger Reserve Director Sanatan Sonkar said.
It was hit from behind by the Nanda Devi Express and left badly injured.
Traffic along the tracks from Dehradun to Haridwar and Rishikesh was disrupted for hours due to the incident as rescuers tried to remove the injured elephant from the railway line.
It was later brought to Chilla range of the Rajaji Tiger Reserve for treatment where he succumbed to injuries, he said.
A post mortem is being conducted on the elephant aged about 20 years after which its burial will take place, he said.
23 wild elephants have died in accidents along the tracks since 1987 between Motichur and Kans Rau notoriously called the "killer track", Sonkar said.
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