The appointment follows a statutory review that started last November. The account was previously held by VCCP.
Initial above-the-line activity will include a regional campaign to push the benefits of rail travel and try to persuade traditional airline users to use GNER services instead.
Moray Shutt, the marketing controller for GNER, said: "CDP presented a focused strategy and well-researched campaign that will unpick the perceptions that plane-users have long accepted, and begin to drive the more lucrative business traveller to GNER.
"In addition, it created the powerful and over-arching thought that is motivating not only for potential and existing customers, but also for staff."
Simon North, the CDP chief executive, added: "The GNER brand is strong and well perceived among users. It is our job to ensure we develop the company's brand attributes while actively driving bums on seats."
Media planning and buying is managed by BLM and is unaffected by the review.
The appointment comes at a busy time for GNER. Earlier this month, the train operator revealed it was to join forces with the Virgin Group and Stagecoach to launch a bid for a stake of the East Coast Main Line service between London and Edinburgh.
A decision will be made by the Government in autumn.