Glenn, a former director at Leicester City, was appointed by the FA in March 2015 and oversaw the men's senior team's rise from a disappointing Euro 2016 campaign to a run to the World Cup semi-finals this year in Russia.
"On behalf of the Board of The FA, I would like to thank Martin for building and leading a senior management team that has transformed our organisation," chairman Greg Clarke said in an FA statement.
"His integrity, commitment, energy and passion for football has underpinned the improvements on and off the pitch. The resulting commercial success has funded hugely significant change in the women's game, St George's Park, the FA Cup and the national teams."
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Glenn's tenure also included World Cup title wins for the under 17 and under 20 teams as well as increasing the body's revenue by 40 per cent.
However, he was unable to secure the sale of Wembley Stadium to Fulham chairman and US businessman Shahid Khan who pulled out of a 600 million pound bid in October.
"I will leave feeling proud of the success of the performance of all the England teams," Glenn said.
"I am confident that we have established in St George's Park, a world class centre which will ensure that the teams will continue to build on their current successes. I hope that The FA will be able to build on this by accelerating the breakthrough of English qualified players into the first teams."
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