First station (1872-1892)

On 1 September 1873 Vlissingen Port was opened on the site of the current station. It was a simple station, mainly consisting of some platforms, and intended mainly for connection to the ferry. At that time the second station of Vlissingen was Vlissingen Town, regarded as the main station. This station was opened a year earlier, on 1 November 1, 1872, and was closer to the centre of town, at the Keersluisbrug along the Canal through Walcheren. The operation of two nearby stations in the port of Vlissingen was too expensive in relation to the limited use, and Vlissingen Town station was closed on 18 July 1894.

Second station (1892-1944)

In 1892 a much larger building was constructed in the style of the Renaissance, whose entrance was located diagonally on the south-west corner. The building included a special waiting room for royalty. The station had three platforms provided with a canopy, of which the pillars and a portion of the canopy remain. The building was inaugurated on 15 September 1894. Five years later, in 1899, however, there was a major incident when a steam locomotive from Amsterdam with faulty brakes broke through the platform and into the station buffet. This accident two conductors' lives.

In 1944 Vlissingen Port was irreparably damaged during a bombing raid.

Third station (1950-present)

Reconstruction took place between October 1949 and September 1950 to a design by architect Sybold van Ravesteyn (1889-1983), whose neo-baroque style is clearly recognisable in the building. The official opening took place on 18 December 1950. Parts of platforms, platform canopy and wall work were retained from the pre-war station. After the war, they also removed the additive 'port' of the name and the station was simply called Vlissingen.

In the eastern part of the main building is a station buffet, with a small raised terrace in front with low stone balustrade. On the west side there is a separate wing with a bicycle facility, behind a free-standing office building. All these parts are attached to the booking hall via the adjacent part of the platforms with each other. The building includes Ravesteyn's characteristic details, like round tilted windows, decorations on the cornices and statues on the facade.

On the outer walls of the station are four ceramic images by Jo Uiterwaal (1897-1972) with representations that refer to the railway and the province of Zeeland. At the entrance of the bicycle facility is the municipality of Vlissingen stone planter with sculpted NS logo and inscription 'Vlissingen 1950'. There is a statue commemorating the electrification of the Zeeland line, manufactured by Philip ten Klooster and unveiled on 17 April 1957.

On the east side of the booking hall were originally ticket offices. In June 2004, these closed, and in late 2010 were replaced by a kiosk. For a long time on the west side of the booking hall there was a bureau de change; after the closure of this at the end of 2001 this part of the station was brought back to its original state.

On 18 March 2010 the station building was designated a national monument and is one of the few designed by Van Ravesteyn station buildings that were not demolished.