Train operator Govia has been given an eight-year franchise to run services across Kent and in parts of Sussex.
South Eastern Trains has been running the service since 2003
The franchise includes running domestic Channel Tunnel Rail Link services.
Govia, which also runs rail firm Southern, will take over from South Eastern Trains which was set up in 2003 after Connex lost its franchise.
The company promises to invest £76m in passenger and staff facilities, and build two new depots in Ashford and Ramsgate - but fares will increase.
Ticket prices are expected to rise by 3% above inflation.
Govia chief executive Keith Ludeman said: "I don't expect they'll be delighted but they should perhaps bear in mind that there is a lot of investment going into the railway - not before time."
The Secretary of State for Transport, Alistair Darling, told BBC Radio Kent the fare increases could be justified.
"I've got to make sure we've got a very good railway service for Kent so we wanted to make sure we have good performance.
"We have already replaced a substantial amount of the rolling stock plus in this particular franchise by 2009 you'll have the first ever high-speed commuter trains," he added.
The franchise area covers Kent and parts of Sussex and London
The South East franchise covers routes connecting Kent and East Sussex with London.
The Strategic Rail Authority (SRA) stripped French-owned Connex of its franchise in June 2003, stating poor financial management as the reason.
It was replaced five months later by South Eastern Trains, a subsidiary of the SRA.
The Rail Maritime and Transport Union (RMT) had argued the region's train services should be kept under public sector control, claiming reliability had improved.
Four bidders were selected to compete for the Integrated Kent Franchise.
They were Danish State Railways, GNER, FirstGroup and Govia, which is a consortium of Go-Ahead Group and Keolis.