The station originally had two platforms, since reduced to one and is served by trains on the Barton line between Cleethorpes and Barton-Upon-Humber, operated by East Midlands Railway.

All services at New Clee are operated by East Midlands Railway using Class 170 DMUs.

The typical off-peak service is one train every two hours in each direction between Cleethorpes and Barton-on-Humber.

[3] On Sundays, the station is served by four trains per day in each direction during the summer months only.

No services call at the station on Sundays during the winter months.