Brown will leave after only 16 months in the role having replaced Ian Ritchie in September 2017, ending a seven-year association with Twickenham which began with his appointment as chief financial officer.
It is understood Brown had grown weary of the internal politics at the governing body and that the decision to resign was his own.
The RFU has been plunged into turmoil by his departure, which comes nine months out from the World Cup and in the wake of stinging criticism from former chief executive Francis Baron.
Baron produced a report accusing Twickenham of financial mismanagement after 64 redundancies were made during the summer despite record revenues being generated for 2016 and 2017. The RFU disputes a number of his claims which are based on its published accounts only.
Brown said: “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 am proud of the people who make up the union.
“I’m sad to leave, but the Union is in good shape, with an excellent leadership team in place.”
Brown declared his rise to chief executive as the “job of a lifetime” upon his appointment only to be ground down by the intrigue at the game’s largest and richest union.
Director of professional rugby Nigel Melville, the Yorkshire-born former England captain, will act as interim chief executive until a replacement is found.
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