Glenn, who joined the FA in May 2015, will leave his role at the end of the 2018-19 season.
He said: “When I accepted the role of CEO at the FA, I was tasked with improving the effectiveness of the organisation and making it financially secure.
“I also joined with the strong belief that the England team’s performance in tournaments could and should improve, and that the experience of the millions of people who play football could be a better one.
“I will leave feeling proud of the success of the performance of all the England teams. 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.”
In a statement the FA said: “[Glenn] has chosen to leave at the end of the season, having delivered much of what he came to do.
“We are extremely grateful to Martin for all he has achieved and he leaves very strong foundations for his successor.”
FA chairman Greg Clarke said: “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.
“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.
“Martin leaves as his legacy an organisation that is fit for purpose, more diverse, internationally respected and ready to progress to the next level.”
Glenn has presided over a series of challenging situations in his role, including the appointment and rapid departure of England manager Sam Allardyce.
He was criticised for his role in the investigation into the conduct of England women’s manager Mark Sampson, who was dismissed in September last year.
And in March he was forced to apologise to the Jewish Leadership Council after referencing the Star of David during the fall-out from the Catalan yellow-ribbon row involving Pep Guardiola.
However, Glenn has also been hailed for increasing the FA’s revenue streams by around 40 per cent, as well as presiding over a significant increase in both profile and participation levels in the women’s game.
On the field under Glenn’s leadership England have enjoyed significant age-group success by winning the Under-17s and Under-20s World Cups.
The senior side under manager Gareth Southgate defied expectations to reach the 2018 World Cup semi-finals in Russia, while the women’s team finished third at their World Cup in Canada in 2015.
In a statement regarding Glenn’s impending departure, the Premier League paid tribute to his “excellent work”.
Premier League executive chairman Richard Scudamore, who will also imminently depart his role, said: “Martin has been excellent to work with over the last four years and deserves huge credit for the continued development of St George’s Park, the successes of men’s, women’s and junior national teams and for prioritising community football.
“During his tenure the working relationship between the Premier League and the FA has been better than ever – as demonstrated by changes made to the football calendar which will see the introduction of a mid-season player break. I wish Martin deserved success for the future.”