It became part of the Merseyrail network in 1994, when the branch from Hooton to Ellesmere Port was electrified by British Rail, and through train services to Liverpool via Birkenhead commenced.

Little Sutton is one of four stations on the Merseyrail network that is Unstaffed, the others being Bache, Capenhurst and Overpool.

The station became part of the Merseyrail Penalty Fares Area on 15 June 2009.

This station is served by trains bound for Liverpool Central and Ellesmere Port, with platform 1 serving Ellesmere Port bound services and platform 2 serving Liverpool bound services, and is classed by Merseyrail as part of the Ellesmere Port branch of the Wirral Line.

Services call at this station every thirty minutes or less, including Sundays.