National Rail said Virgin Trains East Coast services across Yorkshire face delays until 3pm on Tuesday.
It comes after a train derailed at Virgin East Coast's Edinburgh depot at 6.30am this morning.
Network Rail described the derailment as an “operational incident”.
Commuters face disruption this morning as stations including Leeds, Wakefield and Halifax have delays for trains of up to 30 minutes, and cancellations.
Other services being affected include stations in York, Sheffield and Lincolnshire.
There was further misery for commuters after a “fault on a train” outside Keighley halted many services between Skipton, Ilkley, Shipley and Leeds. Network Rail said delays would continue beyond the morning rush hour.
There were also delays to trains Middlesbrough, York and Darlington, and from West Yorkshire to Manchester Victoria.