The section from Nerston to the current station was closed on 24 January 1966, shortly before the last steam-hauled passenger services ceased in March of that year.

Some of the track beyond East Kilbride was in situ until the early 1970s although not in use; photographs as late as 1972 show an overbridge at West Mains Road and the line continuing underneath.

The Caledonian goods shed survived the loss of general freight in the late 1960s and was occupied by scrap merchants until about 1990, then being demolished during redevelopment of the site.

The station is considered to be poorly positioned for modern uses, as it is built near the heart of the old village of East Kilbride, and only partly serves the large new area that has grown since it opened.

The last such proposal in 1989, which involved tunnelling beneath the area around the Civic Centre to reach the new (1986) bus station, was defeated by protests from local 'NIMBY' interests.

[citation needed] British Rail & SPTE also published plans in the early 1980s to re-route services west of Clarkston onto the Neilston branch of the Cathcart Circle Lines using a short-lived connection between the two routes first laid in 1903.

This would have brought overhead electrification to the branch and seen trains run via Muirend and Cathcart to Glasgow, but also seen Giffnock & Thornliebank stations closed (along with the section of line between Clarkston & Busby Junction).