It is part of a bid to drive media coverage and digital activity during its 2015 redevelopment project, Building for the Future.
After winning a competitive pitch, the agency will work on the account on a retainer basis until April 2015.
The project involves a redevelopment of the museum site as well as rethinking every area of its work. Third City will be responsible for communicating the revamp to new and existing audiences and increasing public awareness of what the museum offers.
The main site will be closed for refurbishment until 2016, and during this time Third City will support outreach activity with a focus on news generation around the bicentenary commemoration of the Battle of Waterloo.
The agency will report to the museum’s head of marketing and comms, Rebecca Hubbard, who said: "Next year is huge for us as an organisation and will involve major changes in the way we communicate - both through the media and to the public directly. We feel Third City really understands the challenge we face and has the right combination of energy, expertise and insight needed to support us in this venture."
Associate director Chris Blackwood will head up the account team. He said: "With communications central to conveying the new direction the museum is moving in, there couldn't be a more exciting time to come on board."