The Newquay to Par branchline has been re-opened after engineers worked overnight on Wednesday to clear a train and its carriages from the track.
The tractor driver was airlifted to the Royal Cornwall Hospital
The Wessex train involved in the collision with a tractor on the level crossing at Cosworth on Tuesday has been taken to St Blazey for repairs.
An investigation is continuing into the collision which left the 20-year-old tractor driver seriously injured.
The crossing remains closed to vehicles.
No one else was seriously hurt following the accident near Quintrell Downs in Cornwall.
Traffic on the unclassified road is controlled by an audible signal and warning lights, switched on by approaching trains.
The operation of the lights and signal, similar to other crossings on the line, will form part of the investigation.
It is the fourth collision on the Newquay to Par line this year. Network Rail has ruled out erecting barriers at the crossing.