The Network Rail contractor was hit by the 11.19am service from Scunthorpe to Lincoln, operated by Northern Rail.
The fatal collision happened at Sykes Lane near Saxilby station just before 2pm.
Network Rail confirmed a contractor working on their behalf had been ‘fatally struck’.
A spokesman said: “Investigations are ongoing into what happened but our thoughts are with the family.”
It is thought the man was aged 26 and from the Doncaster area.
British Transport Police, Notts Police and the Rail Accident Investigation Branch continue to investigate the incident.
The line between Gainsborough Lea Road and Lincoln was closed for several hours.
Trains are now running as normal between Lincoln and Gainsborough Lea Road.
However, East Midlands Trains are running replacement buses between Lincoln and Doncaster after a separate incident at Finningley yesterday.