He threatened legal action if the results of a report into the dismissal of predecessor John Steele were made public and has faced widespread criticism ever since.
Former RFU chairman Thomas will also leave his posts asEuropean Rugby Cup Ltd director, International Rugby Board Council member, Six Nations Committee member and chairman of England Rugby 2015, the organisation in charge of England's staging of the next World Cup.
Thomas will oversee a transitional period at the RFU until leaving on December 16 when chief financial officer Stephen Brown will take over as acting chief executive, although news of a permanent appointment is expected two days earlier.
"It has been an honour to be part of the Union, most particularly for the past six months as acting chief executive where I have been lucky enough to get to know better the RFU staff who work tirelessly for the good of the game," read a statement from Thomas.
"Stephen Brown for one has been a phenomenal addition to the executive team and, having got to know him very well over the last few months, I have total faith that he will provide the stability and leadership needed at this important time."
The move has been welcomed by former England international and ex RFU council member Simon Halliday, who sees Thomas' departure as a move in the right direction for English Rugby.
"You can draw a huge line in the sand now," Halliday told BBC Radio Five Live.
"It's tempting to look back over the last seven years of his tenure, but I prefer to look forward and regard this as the first step to getting English rugby back to the sort of state it should be in."