The station is located 59.5 miles (96 km) south of Bristol Temple Meads, on the Heart of Wessex Line.

The station was opened by the Great Western Railway (GWR) as part of the Wilts, Somerset and Weymouth route on 1 September 1856.

Great Western Railway operate the majority of services at Pen Mill on their route between Weymouth and Gloucester, via Bristol Temple Meads.

[11] South Western Railway operate a few services between London Waterloo and Pen Mill, some via Yeovil Junction and others via Westbury.

Commencing in December 2015, a limited regular passenger service began using the connection between the two lines.