It is both a terminus of the Wirral Line, a commuter rail system operated by Merseyrail and of Northern Trains services to Warrington Bank Quay.

[2] Ellesmere Port became part of the Merseyrail network in 1994, when the line from Hooton was electrified by British Rail and through train services to Liverpool's city centre via Birkenhead commenced.

Liverpool City Region Combined Authority, Long Term Rail Strategy document of October 2017, page 37, states that a trial of new Merseyrail battery trains will be undertaken in 2020, in view to extend the Wirral Line branch terminal to Helsby.

Platform 2, for Northern services, can be accessed by a passage alongside the staircase on Whitby Road.

Merseyrail Wirral Line services operate every 30 minutes each day (including Sunday) towards Birkenhead and Liverpool.

[8] No services stop at Stanlow, due to the poor condition of the station footbridge.

The evening service from here continues beyond Helsby to Liverpool Lime Street via Warrington Bank Quay.