Rapier beat Saatchi & Saatchi and Liquorice in the final round of the contest.
The agency's first work will be a spring campaign, running across on- and offline media, to encourage consumers to take the train when they go on a leisure excursion.
Janet Somerville, South Eastern Trains' commercial director, said: "Rapier's campaign demonstrated a clear understanding of our business and our customers' needs.
"South Eastern Trains is widely known as a commuter train company. We are keen to exploit the leisure market and Rapier's campaign provides the ideal platform."
John Townshend, the Rapier executive creative director, said: "South Eastern Trains has made tremendous efforts to improve rail travel since taking over the franchise. Our new campaign builds on these foundations and brings them to life in a single-minded creative vehicle."
South Eastern Trains operates services across South- East London, Kent and parts of East Sussex. The previous operator, Connex, was stripp-ed of its franchise for the area last November after it struggled with issues of overcrowding and late-running trains.