Glenn, a former director at Leicester City, was appointed in March 2015 and oversaw the men's senior team's rise from a poor 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," FA chairman Greg Clarke said in a 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 (development centre), the FA Cup and the national teams."
Glenn's tenure also included World Cup title wins for the men's under-17 and under-20 teams, and a 40 percent increase in FA revenues.
However, he was unable to push through the sale of Wembley Stadium to Fulham chairman and U.S. 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."
Alongside the highs, Glenn also came in for criticism last year for his handling of complaints by senior female players Eniola Aluko and Drew Spence that they had been subject to racism and bullying from former England women's team boss Mark Sampson.
Two independent investigations cleared Sampson of racism and bullying but he was ruled to have made discriminatory remarks, leading to a public apology from Glenn to the two players.
There was also the embarrassment of sacking England men's manager Sam Allardyce in 2016 after 67 days in charge following a newspaper report that alleged he had advised undercover reporters on ways to circumvent restrictions on third-party ownership of players.
Nevertheless, that decision led to the appointment of Gareth Southgate, who led England to fourth place at the World Cup in Russia and then a place in the final four of the inaugural European Nations League, reviving the country's enthusiasm for international football.
(Reporting by Christian Radnedge; Editing by Kevin Liffey)
