Ince station was opened on 1 July 1863 by the Birkenhead Joint Railway. It was renamed Ince & Elton on 17 April 1884.
Services were operated jointly by the London and North Western Railway and Great Western Railway up until the 1923 Grouping, then by the GWR and the London, Midland and Scottish Railway. After nationalisation in 1948, the station became part of the London Midland region of British Railways.
The route through the station carried significant amounts of freight from the outset, from the docks at Birkenhead and later from the oil refineries and dock complex at Ellesmere Port as well as a local passenger service between Birkenhead Monks Ferry (from opening until March 1878)/Birkenhead Woodside (from April 1878) or Hooton and Helsby, where passenger could access the other section of the joint line between Warrington Bank Quay and Chester.
This station was earmarked for closure, along with Stanlow and Thornton, Helsby and Ellesmere Port, under the proposals made by Dr. Beeching. This was never implemented, although services gradually began to reduce and the remaining through trains to/from Birkenhead Woodside ended in 1967 when the station there was closed.
Services originally operated regularly between Helsby and Hooton via Ellesmere Port, with some services running through to Rock Ferry prior to the electrification of the line between there and Hooton in 1985. Once electric trains began running to Hooton, the service was revamped to run between Chester and Helsby via Hooton (with a reversal there) every 30 minutes on weekdays and Saturdays.
Convenient connections were available at Helsby for Warrington and Manchester and at Hooton for Liverpool. However, following the extension of the third rail southwards to Chester in 1993, the service east of Ellesmere Port was cut back substantially – most trains ran as a shuttle to Ellesmere Port only, with only a two-hourly service beyond there.
The pattern was then altered again when electrification of the Hooton to Ellesmere Port section was completed in 1994 – from that point onwards, all services from Helsby terminated at Ellesmere Port but ran beyond Helsby to Warrington Bank Quay and Liverpool Lime Street.
The new service was poorly patronised though, and by 1996 it had been cut back to the current pattern of two pairs of services each way in the early morning and mid afternoon as it remains today.