The station was opened in 1849 on the former main line of the Great Grimsby and Sheffield Junction Railway which became part of the Manchester, Sheffield and Lincolnshire Railway.

The footbridge and Grimsby bound platform have since been removed and the route reduced to a single track at this point.

[2] All services at Kirton Lindsey are operated by Northern Trains.

As of 21 May 2023, this station is served by only two trains per day on weekdays only, one to Sheffield and one to Cleethorpes.

[3] Between October 1993 and May 2023, the station was served by 3 trains in each direction between Sheffield and Cleethorpes on Saturdays only, with no services running on weekdays or Sundays.