The pachyderm was killed when it was hit by Sampark Kranti Express, police said.
As the train was speeding, the male tusker was hit hard and died on the spot, police said.
Police said they have arrested a number of passengers who got down the train and tried to remove the tusks of the dead elephant after the incident stopped the train.
The railway line which connects north Bengal to the neighbouring Assam cuts through the reserved forest area in Jalpaiguri's Alipurduar sub-division where such elephant deaths have been reported regularly.