Storey, who is 40 next year, is taking a year out and is on a six-month period of gardening leave.
He said: "I've been busy for the past 20 years and before I do the same for the next 20 years, I'd like to spend some time understanding what I have done and preparing for what I would like to do."
Since joining from Benton & Bowles, Storey has held a number of senior roles for the company, including running the UK business, large-scale account handling, pitch adjudication and, most recently, handling international new business.
Last year, Storey was part of a management buyout led by the former senior Guinness marketer, Julian Spooner. It also included Michael Cluff and Mauricio Barange.
Media Audits' chief executive, Spooner, said: "John's passion and commitment are legendary in the media business. He has been a major force in driving Media Audits. My colleagues and I wish him every success in the future."