The crash affected services running between Wakefield Westgate and Leeds.
A broken down train between the two stations added to the problems.
Network Rail engineers inspected the bridge and lines reopened at around 8.30am, but National Rail was warning trains may be delayed or cancelled as services return to normal.
Disruption was expected to continue until at least 9am.
Cross Country, Northern and and Virgin Trains East Coast services between the two stations were all being disrupted.