The underground, low level station consists of a single platform, alongside the Liverpool Loop tunnel, a single track tunnel bored in the 1970s, and a ticket hall above. The station, opened in 1977, is connected to the mainline station by means of a pedestrian subway and escalators, accessed via a long passageway which crosses beneath Lime Street itself, and by a lift from the main concourse.
As part of a programme of improvements by Merseytravel, the underground station has been fitted with automatic ticket barriers and machines.
Network Rail announced in early 2013 that Lime Street was to be the third station to be refurbished as part of the £40 million investment which would see all Merseyrail underground stations excluding Conway Park refurbished. This included the refurbishment of the platform and the booking hall. The station refurbishment work took place between April and August 2013.
The subway linking the underground station to the mainline station was refurbished in June 2014. The subway was fitted out with new tiles, lighting, flooring and automatic doors to some of the entrances.
The underground station had WiFi installed in January 2016.
In March 2016, it was announced that the Wirral Line loop would be having its track renewed. The underground station was closed between 3 January 2017 and 18 June 2017 whilst the works took place.
Services operate on a 5-minute frequency Monday-Saturday, and between 5- and 10-minute frequency on Sundays in the winter. All trains travel through to Liverpool Central and Birkenhead of which:
4 trains per hour continue to New Brighton
4 trains per hour continue to West Kirby
4 trains per hour continue to Chester
2 trains per hour continue to Ellesmere Port
To reach destinations on the Northern Line of the network, passengers must either use the Wirral Line and change at Liverpool Central station or walk the short distance to the station.