The Bury line ran northward from the junction, crossing the Irwell Valley on the Clifton Viaduct (known locally as the "13 arches"), to run on the opposite side of the valley from the Bolton line. A station at the junction, with two platforms for each route (Bolton or Bury), opened in June 1847, and was named Clifton Junction.[2][6]
The line to Bury closed in 1966 along with the platforms that served it, with the tracks being lifted in 1968.[7] The old Bury and Accrington platforms are still intact (though heavily overgrown) in the woodland that now occupies the site of the junction behind the modern station, and the viaduct remains a Grade II listed local landmark.
On 6 May 1974 the station was renamed Clifton,[6][8] (even though the area has become known as Clifton Junction), and in the 1990s the service was reduced to one train per day in each direction.
The closest station to Clifton Junction with a regular service is Swinton 1.25 miles (2.01 km) away on the line between Manchester and Wigan Wallgate via Atherton.
The service at Clifton railway station is very limited in the current 2023 timetable (and has been since 1992),[9] with just one train calling in each direction between Stalybridge and Southport per day - southbound (at 08:36) in the morning peak and northbound (at 18:20) in the evening. In 2012, the station had only a small amount of services day in each direction (local services run by Northern); only 170 passengers were recorded as using the station in 2010–11. The single daily service each way was suspended between May 2015 and the December 2015 timetable change due to the ongoing modernisation work at Farnworth Tunnel, with a replacement bus provided instead. The station reopened on schedule on 14 December 2015.