Former editor of The Independent Ian Hargreaves will leave the FCO when his two-year secondment comes to an end in late May.
Until a successor is appointed, Hargreaves' duties will be handled by FCO director of strategic comms Conrad Bird and head of news Carl Newns.
Hargreaves joined the FCO in 2008 on a two-year secondment from Ofcom, succeeding Lucian Hudson. Foreign secretary David Miliband is said to have charged Hargreaves with shaking up the FCO's communications structures.
Before Ofcom, Hargreaves was group director of corporate and regulatory affairs at BAA. He also edited New Statesman and was deputy editor of the Financial Times.
After his departure, Hargreaves will handle a portfolio of freelance work, including journalism, communications consultancy and academic work. He will be based at Cardiff University, where he still holds an academic position.