The incident at Fitzwilliam near Wakefield closed main lines for 50 minutes but caused knock-on delays through the afternoon.
Many Virgin services from London were diverted from Leeds to York.
Network Rail warned of delays of up to 120 minutes on journeys between Doncaster, Sheffield and Leeds, with disruption expected to continue until 5pm.
Police said there were no suspicious circumstances to the incident.
Earlier in the day, trains were delayed between Bridlington and Scarborough after a vehicle hit a bridge between Bridlington and Filey.