The grill, Burrito and Taco specialist has taken on the lease for a building in St Martin's Lane, previously occupied by St Martin's Spice.
It is Chipotle's second signing in London in as many weeks and is part of major expansion plans for the brand in the UK this year. Last week it signed on a site in Soho's Wardour Street.
Nick Weir of Shelley Sandzer, who acted on behalf of the building's landlord, said: "Chipotle's brand of fresh, sustainable ingredients prepared using classic Mexican cooking methods is set to become a big hit in the capital this year.”
Chipotle opened its first restaurant in 1993 and currently operates more than 1,000 restaurants around the world. Its first UK restaurant opened on Charing Cross Road in 2010 with a site in Baker Street opening in September 2011.