Southgate is leaving his post as the FA's head of elite development and has said he no longer wishes to be considered for the role of technical director.
Southgate said in a statement: "I'd like to place on record just how much I've enjoyed working at The FA over the past 18 months. It really has been an honour and a pleasure. Hopefully, I have been able to play some part in delivering important changes to the way children play at the youngest levels.
"The FA is heading in the right direction in terms of developing more, better coaches and players at all levels of the game under the leadership of David Bernstein, Alex Horne and Sir Trevor Brooking. I would like to thank them for their support throughout my time with the organisation.
"I've advised The FA that I will be pleased to help with specific projects moving forward".
Southgate, who played a significant role in developing the plans and facilities for the new national football centre at St George's Park and worked on implementing the Elite Player Performance Plan, who will continue to work as a pundit for ITV.
FA general secretary Horne added: "Gareth has made an outstanding contribution in supporting Sir Trevor Brooking and myself across various aspects of our football development work over the last 18 months.
"We're disappointed, but understand his decision and would like to thank Gareth for his efforts and wish him well for the future.
"We continue to recruit for key technical positions within The FA at what is a very important and exciting time for the organisation, with the imminent opening of our new training centre at St. George's Park."