Clifton, who was the head of strategy and planning at AKQA, will be responsible for building and strengthening Agency.com's planning capabilities for its offices in London, Amsterdam, Brussels, Paris, Dublin and Milan.
Clifton will work closely with the European creative director, Paul Banham, and take a key role as the agency looks to expand its offices through acquisition. He will report to Agency.com's worldwide chief executive, David Eastman.
Eastman said Clifton will "play a huge part in establishing a strong strategic planning practice across our newer European offices".
Clifton said that his role is part of Agency.com's strategy to "look seriously at the European remit".
He added: "Agency.com is growing, and now that it has a few European offices, there's a need for someone to oversee and take an overarching responsibility for the planning disciplines across Europe.
"Ultimately, the challenge will be to look at how the agencies vary in each market and plan accordingly."
Clifton will be based in London, but will work with the senior management in each office to ensure the quality of work is consistent across the European region.
Clifton has more than eight years experience in digital, and this appointment sees him return to Agency.com, where he worked as a planner for four-and-a-half years. He's worked on clients that include Coca-Cola, Nike and Yell.