The incident affected LNER, Transpennine Express and Cross County services.
All lines were closed to allow emergency services to attend the incident safely.
Passengers have been warned by service providers that train services between these stations may be canceled or revised.
Meanwhile, major disruptions are expected on these lines by the end of the day.
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An LNER spokesman said: “A man has been hit by a train between York and Darlington. All lines are currently closed to allow emergency services to deal with the incident safely.
“Trains running between these stations may be canceled or revised.
“Major disruptions are expected by the end of the day.”
“If you’re affected by what happened online today, there’s always someone to talk to. You can contact the Samaritans on 116 123 from any phone for a confidential chat.
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“Customers who wish to postpone their journey tonight and travel tomorrow, Monday 20 February, can do so using their original tickets.”
The LNER has advised that the buses replacing the rail should operate as follows:
2 York Pullman buses will run between York and Northallerton
2 York Pullman buses will run between York and Darlington