The station was formerly called Stonehouse Burdett Road to distinguish it from a second station, Stonehouse (Bristol Road), on the line between Bristol and Gloucester. Stonehouse Bristol Road closed to passengers under the Beeching Axe in 1965 and to goods traffic the following year.
The station has two platforms, and is operated by First Great Western. The station has a ticket office, located on the Gloucester-bound platform; it is normally only open in the mornings, until the end of the peak period.
The platforms are short: only about 55 yards (50 m) each. This is long enough to accommodate the two-coach trains used on Swindon – Cheltenham Spa local services; but trains running to or from London or Worcester may be up to eight coaches. Since long trains cannot be accommodated entirely, such trains running towards Gloucester normally stop with the front two coaches in the platform, and those running toward London normally stop with the rear two in the platform. Passengers intending to alight at Stonehouse are advised earlier in their journeys to proceed along the train to the relevant coaches. Since trains from Cheltenham almost always reverse at Gloucester, this can lead to confusion for cyclists as to which end of the train in which to load their bicycles.