Northern Rail reported a fault with the signalling system at Leeds City Station at 6.48am, blocking some train lines.
By 7am all lines had reopened but a number of Northern Rail services have been cancelled.
Trains will continue to be delayed or amended at short notice as services return to normal.
Some LNER services running through Leeds are delayed by up to 15 minutes.
Northern Rail apologised to customers for the "severe" delays.
List of Northern cancellations
06:55 Huddersfield to Leeds due 08:02
07:18 Nottingham to Leeds due 09:15
07:37 Ilkley to Leeds due 08:05 has been cancelled.
07:45 Leeds to York due 09:01 has been cancelled.
08:26 Leeds to Skipton due
09:11 York to Leeds due 10:23 will be cancelled.