The appointment was made after a competitive pitch, which began in July and was overseen by Creativebrief.
The agency will handle the launch of a new mainline service for the rail operator, which will run between Oxford Parkway and London Marylebone.
Connect Group was the incumbent of the business. It was behind the operator's two straplines, "If you think our way, travel our way" and "Nice and fast".
Thomas Ableman, commercial director of Chiltern Railways, said, "The Gate’s overall strategic approach is ideal for a challenger brand like Chiltern Railways.
"We were impressed by the team’s creative thinking, energy and felt immediately that they had the insight to help us achieve our very challenging targets in one of the most crowded travel markets in Britain."
Christy Stewart-Smith, managing director of The Gate London, said: "Chiltern Railways is already the UK’s highest rated train operator, because they’ve focused relentlessly on the things that matter most to customers.
And their new service from Oxford Parkway is the first new rail link between London and a major British city in over 100 years. It will give rail passengers a real choice on how they travel. We’re very excited to be involved."
Chiltern Railways is owned by Deutsche Bahn and is part of Arriva, which runs Deutsche Bahn’s services outside Germany.