Dramatic pictures of the tractor that blocked a train line near Wakefield have emerged, showing damage to the line's infrastructure.
Network Rail engineers together with the emergency services worked through the night to remove the tractor and carry out emergency repairs.
Some services were able to resume running at 10:30 and this was followed by a full service on the lines from 13:00.
Electric trains operated by London North Eastern Railway are currently coasting through the affected area prior to further engineering work taking place overnight.
Tonight (Thursday) Network Rail engineers will begin further engineering repairs which once complete, will allow electric trains to travel through the affected area as normal.
More delays expected
A spokesman for Network Rail said: "Due to the nature of the incident, residual delays are expected so passengers are urged to check their journey ahead of time via National Rail Enquiries or with their train operator.
"We are sorry for any disruption and we'd like to thank passengers for their patience today."
The tractor was said to have breached the boundary of a nearby field late on Wednesday evening.
The tractor has now been removed from the line at Fitzwilliam, but trains have been disrupted, delayed and cancelled throughout the day.
Services in and out of Leeds, Wakefield, Sheffield and Doncaster, among others, were disrupted, with major delays in place.