The incident, between Shipley and Guiseley, means all railway lines are currently blocked between these stations.
Disruption is expected on all routes in the Shipley, Bradford Forster Square and Ilkley areas, with no trains currently running between Bradford Forster Square and Ilkley.
Train operators expect a “good service” will be operating by about 9.30am.
A spokesperson for British Transport Police said: “British Transport Police attended the line close to Baildon railway station after reports of a man being struck by a train.
“Officers from British Transport Police and West Yorkshire Police were called to the scene following a report to police at 6.43am and the death is currently being treated as non-suspicious.
“Paramedics and the local ambulance service attended but the man was pronounced dead at the scene. A file is being prepared for the coroner.”
The incident involved the 6.15am service from Bradford Forster Square to Ilkley.
Passengers travelling from Bradford Forster Square are being advised that they can circulate via Leeds for services back to Ilkley.
Replacement road transport has been requested to operate between Shipley and Guiseley departing at 7.30am and 8.10am, and from Guiseley to Shipley at 8.15am.