The station was opened by the London and South Western Railway as a temporary terminus when its line to Southampton reached Basingstoke from London. It became a through station when the section running north from Southampton was completed later in 1840. The intention to build a line from near Basingstoke to Bristol was dropped when the Great Western Railway was approved. The L&SWR did, however plan a line to Salisbury from Basingstoke but this was delayed by financial difficulties. Eventually, it was built reaching Andover in 1854 and Salisbury three years later, before being extended to become the West of England Main Line.
The Great Western Railway opened its broad gauge line from Reading on 1 November 1848 with a separate station north of the L&SWR station. After its conversion to mixed gauge on 22 December 1856 through services could run between Southampton and Reading. The broad gauge rail was removed on 1 April 1869. The GWR station was closed on 1 January 1932 demolished in 1932, since which trains from Reading have used the main station.
Basingstoke station was the terminus of the Basingstoke and Alton Light Railway, opened in 1901 to prevent the GWR from building a line on this route towards Portsmouth. The line was never profitable. During the First World War some of the track was sold off. After the war, Southern Railway had the line reopened, but it was closed finally in 1932.
In the 1980s Platform 5 was converted to a bay platform to permit an entrance on the northern side by British Rail. In 1993, an explosive device planted by the Provisional Irish Republican Army was found in a toilet, soon after a bomb scare at Reading railway station.[6] In 2001 a suitcase was left outside the station containing the mutilated body of a man in his twenties. He had been stabbed to death.
Anglia Railways ran the London Crosslink service from Ipswich to Basingstoke via Stratford and the North London Line using Class 170s between May 2000 and September 2002. South West Trains also ran a local service from Reading to Brighton until timetable changes on 9 December 2007. Southern railway services from Southampton and Portsmouth to Brighton were improved to compensate for that.