Brown succeeded Ian Ritchie in September, 2017 having worked at the RFU since 2011, mainly as chief financial officer during which time he oversaw the hosting of the financially successful 2015 World Cup.
Recently, however, things have not gone so smoothly, with the redevelopment of Twickenham's East Stand going way over budget and the union announcing 64 redundancies as part of a cost-cutting exercise.
Francis Baron, CEO for 12 years until 2010, has produced a long report into the union's finances and condemned what he described as poor financial management.
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The RFU, which runs the game from England international level down to grass roots and schools, responded earlier this week by questioning Baron's figures and saying it was "on a sound financial footing, with a healthy cash position, robust contracted revenues and a good balance sheet."
Brown said in a statement on Friday: "This has been a very difficult decision for me to make, and I informed the RFU Board earlier this week that the time is right for me to step down and take some time out.
"I’ve loved my time in rugby and am deeply proud to have made a contribution to a sport I love. It has been a fascinating seven and a half years, and a great honour to lead the RFU over the last 14 months.
"I'm sad to leave, but the Union is in good shape, with an excellent leadership team in place."
RFU Chairman Andy Cosslett described Brown as a "pivotal figure during a long period of sustained growth for the Union.
"As Managing Director of the Organising Committee he played a key role in delivering Rugby World Cup 2015... the success of the tournament returned a wonderful dividend for the RFU and left a lasting legacy."
Nigel Melville, Director of Professional Rugby, will act as interim CEO until a new appointment is made.
(Reporting by Mitch Phillips, editing by Andrew Heavens and Toby Davis)
