It is 70 miles 30 chains (113.3 km) from London Liverpool Street and is situated between Waterbeach and Littleport stations on the Fen line to King's Lynn.

Ely is a busy station with trains running to a variety of destinations including London, Cambridge, King's Lynn, Birmingham, Nottingham, Sheffield, Manchester and Liverpool.

It is managed by Greater Anglia, which is also one of four train operators that serve the station, the others being Great Northern, CrossCountry and East Midlands Railway.

[4] The level crossing existed because the underbridge had limited clearance so taller lorries had to travel this way sometimes causing delays to the railway services.

On 1 November 2018 following the opening of the Ely bypass, the level crossing immediately north of the station was closed to road traffic.

Ely was the start point for some local stopping services to March, Newmarket, King's Lynn and Norwich, as well as the branch line to St. Ives.

Longer distance services all called at Ely, although one exception was the 11:20 London St Pancras – King's Lynn and Hunstanton.

Ely was served by the Hook Continental service from Harwich Parkeston Quay to various destinations in the North and Midlands.

After that, an outbased Cambridge diesel shunter took care of shunting duties in the area until the early 1990s; when not in use, this was stabled in a short siding adjacent to the station.