Brooks, who is also a director of Guardian Media Group, will leave at the end of March, after which commercial members of the GNM executive committee will report directly to GMG chief executive officer Andrew Miller.
Brooks joined GNM in August 2006 from IPC Media, where he was managing director of men's lifestyle and music division IPC Ignite.
Before IPC, he spent nine years in senior management at Emap, including a stint as network managing director within Emap's UK business and as executive director of Emap Digital. He also co-founded Media Week magazine.
Andrew Miller said: "On behalf of the GMG board I would like to thank Tim for everything he has done for GNM and the wider group over the last four and a half years.
"He has been a passionate and dedicated servant of the company and its journalism, he has played a crucial role in the Guardian’s ongoing digital transformation, and he has led the business with great integrity at a time of significant change and sometimes difficult choices. He leaves GNM with our best wishes for the future."
Brooks said: "The best aspect of my work here has not been husbanding two of the finest news brands in the world; it has been the chance to work daily with the extraordinarily gifted and committed people of GNM. I will miss that greatly, and continue to consume their output with familial pride."
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