Jolly has been comms director for more than two years. Before the MoD, he was director of external affairs and comms at the University of Cambridge.
Last year Jolly oversaw a review of comms across the nine 'functions' of the nation's defences, including the Army, the Royal Navy and the Royal Air Force. Jolly's key ambition was for the MoD directorate to have stronger central power, with a greater capability in content creation and digital communication.
Alex Aiken, executive director of government comms, said: "At MoD, Stephen's reform of defence communications has been radical and ambitious. Wide-ranging governance reforms, digital ways of working and a full spectrum approach to communications that encompasses military influence operations as well as traditional public relations activity have been some of the innovations he has introduced.
"We want to harness some of that radicalism and ambition. Stephen has already made a strong contribution to the Government Communication Service. As a member of the Government Communications Board, he has worked hard to ensure that defence communication has been represented effectively across Whitehall in areas such as reserve recruitment, Scotland, the cross-government economic campaign and Ebola."
From September, Jolly will become senior research fellow in Military Information Operations at the Defence Academy. Until then he will work alongside Aiken at the Cabinet Office for two months, working on a number of projects.