In 2001 the Strategic Rail Authority refranchised the South Central franchise, then held by Connex. The franchise was won by Govia who bought the remainder of Connex’s franchise time and began operating under the Southern brand from 28th August 2001.

Southern was responsible for operating train services, whereas Network Rail owned and managed the infrastructure such as stations and track, the trains themselves were leased from rolling stock companies.

Part of the franchise commitment was the replacement of the MK1 slam door EMUs with new stock. This led to the introduction of the class 377 and the replacement of the older stock by 2005.

Southern was headed by David Franks until 2003, who was replaced by Charles Horton who in turn was replaced by Chris Burchell in 2006. The headquarters were based in Bristol.

Southern ran was responsible for the services from London Bridge and Victoria to South London and Sussex. The company used a green livery with a yellow roundel to recall the pre nationalisation railway company.

In 2007 the Department of Transport announced that the Gatwick Express franchise would be merged with Southern, although the separate brands would be retained. This occurred in May 2008 and it was decided that the refranchising would be moved forward to September 2009.

In 2014 the Thameslink 2000 the government decided to merge the Southern franchise into the newly enlarged Thameslink, Southern and Great Northern franchise. This occurred on 26th July 2015 although the Southern and Gatwick Express brands were retained.