Rail company Northern said that journeys between the two cities that go through to Preston are currently not operating due to problems with a level crossing.
A replacement bus service is operating between Selby, York and Leeds, stopping at Church Fenton and Ulleskelf.
The disruption is expected to continue through the morning rush hour until around 10.30am, the company said.
For up to date information go to https://www.journeycheck.com/northernrail/.