The line opened on 1 August 1874, with Port St Mary as a flag stop on the way to Port Erin. The original station was a small timber structure with a zinc roof, very similar to the surviving small wooden buildings at Santon and the lost ones at Ballasalla and Colby. As the village's popularity as a resort grew through the 1880s and 1890s, the railway company decided to upgrade. In 1898 a local firm constructed today's building, a substantial two-storey block with a central recessed shelter flanked by waiting rooms and staff accommodation. Tickets, refreshments, a ladies' waiting room, and a porter's hall all operated from the building. It is the only proper station on the surviving line without a passing loop, simply because the next station, Port Erin, is so close that nobody needs to pass anyone here.

Beside the station, in the same handsome local rubble stone with red brick quoins, stands the 1902 goods shed. It is built to the same plan as the surviving shed at Castletown. Rail-connected doors at either end allow a wagon to be shunted right through; platform-height openings on the side let goods be loaded directly onto trucks. For much of the twentieth century it was a working freight building. Then in 2020 the railway began using it for the decontamination of asbestos from non-service locomotives. In 2022 the goods shed became the volunteer base for the Isle of Man Steam Railway Supporters' Association, and the locomotive No. 5 Mona was moved in for cosmetic restoration. The interior of the shed has also been a film set: it was dressed as Burnett Stone's workshop on Muffle Mountain for the year 2000 film Thomas and the Magic Railroad. The Manx engines did not actually appear in the film, but the shed did, repainted and refitted by the film's set-builders, who then left the doors and lighting better than they had found them.

The main station building has had a chequered second life. From 1982 to 1989 an outdoor pursuits company called Campamarina leased the upper floor and converted it into hostel accommodation for their Trailblazers holiday scheme. The booking hall got a servery and a new fireplace; shower rooms went into the back. Railway staff were exiled to a wooden shed on the platform. When Campamarina left in 1989 the station drifted, occupied intermittently, never quite finding its purpose. In 2008 a developer was granted permission to convert it to apartments; the project never happened. In 2012 it was sold for office conversion; that application was denied for lack of parking. A proposed toy museum in 2018 also failed to materialise. In summer 2014 the station became unstaffed except for the toilets and waiting area; in 2020 even the toilets were closed for being in too poor a state of repair. The building still stands. It is open. It is empty. It is waiting for the next idea.

For a small village station, Port St Mary has appeared on screen a surprising number of times. The exterior featured in a night shoot for the Channel Four Cinderella in 2001, with the locomotive Caledonia in her deep blue livery. The BBC drama The Ginger Tree filmed here in 1989. The 1999 film The Brylcreem Boys used the station. The 2003 TV movie Legend of the Tamworth Two had scenes here, as did the year 2000 film Thomas and the Magic Railroad in its goods shed. The strangest credit: in 1979 the BBC variety show Seaside Special used the station platform as a stage for a dance routine to Chattanooga Choo-Choo, with the train, the platform, and the goods shed pressed into service as a chorus line. Anyone who watched television in 1979 may already have seen Port St Mary station and not known it.

Like several of the smaller Manx stations, Port St Mary's is not in the village. It sits half a mile from the heart of Port St Mary, having been built where the railway company chose to put the line rather than where the village would have wished. From the platform you walk down a slight slope past the Station Hotel and the new housing estate on the old gasworks site, demolished in 2012. Then the village proper begins: lines of small shops, the chip shop, the post office, and the road down to the harbour. The walk is about ten minutes. Many train passengers do it specifically to pick up the Raad ny Foillan, the Way of the Gull coastal path, which runs past Port St Mary in both directions and can be followed all the way to Port Erin and the Sound. The bilingual nameboards now read Stashoon Raad Yiarn Phurt Le Moirrey, Port St Mary railway station, in maroon and cream. The cream is freshly painted. The train will be back in an hour or two.