The Thomas Lane tunnel was located on the Cheshire Lines Committee Railway (CLC) North Liverpool Extension Line that connected the CLC Liverpool and Manchester line at Halewood to Aintree and via a branch to the north Liverpool docks at Huskisson Dock. The CLC was a joint railway with three partners, the Great Northern Railway (GNR), the Manchester Sheffield & Lincolnshire Railway (MS&LR) and the Midland Railway (MR). All had wanted access to Liverpool which by the mid-19th Century had become a major seaport. The CLC Liverpool and Manchester line which opened on 1 August 1873 had given the three companies' access to Liverpool but only to the south docks. To north of the city new docks had been built that could take much larger vessels. The London North Western Railway (LNWR) and the Lancashire & Yorkshire Railway (LYR) had access to the north docks and the CLC partners wanted the same. The most logical way for the CLC to gain such access would have been for them to extend their Liverpool and Manchester line by three miles from its Liverpool terminus. However this would have involved tunneling under the city centre which would have been prohibitively expensive. The alternative solution was to build a line around the eastern edge of the city using agricultural land that was by the 1870s very cheap. The only significant engineering that would be required was at Walton north of Liverpool. The North Liverpool Extension Line and its branch to Huskisson was authorised on 30 July 1874 and opened from Halewood to Walton-on-the-Hill for passenger services on 1 December 1879.
A tunnel was required at Thomas Lane to carry the line under a crossroads. An interesting feature of the North Liverpool Extension Line which was a double track railway was that the infrastructure was laid out in a way that would make quadrupling the line at a future date an easy task. Over bridges were built with double arches capable of taking two tracks through each. The cuttings and embankments were only made to accommodate two tracks although enough land was purchased to allow for widening.
For this reason two parallel tunnels were built at Thomas Lane. Only the east bore was brought into use. The west bore would never be used.
The line went on to become a major freight artery to the Liverpool docks and from 1884 an extension was opened to Southport. It went into decline in the second half of the 20th century. The Thomas Lane tunnel saw its last regular passenger trains on 5 November 1960 (Although excursions ran for a period after that date). On 21 October 1972 the line through the tunnel was singled. The last freight trains ran in May 1975 and the line was taken out of use in August 1975. It was lifted in the early months of 1979.
In the late 1980s the Liverpool Loop Line path part of the Trans Pennine Trail opened through the tunnel.