Lee originally joined England in July as part of Sam Allardyce's backroom staff, having also worked with the Three Lions during Sven-Goran Eriksson’s spell in charge.
Lee stayed in his role following Allardyce's shock departure earlier this year but will now move on as Gareth Southgate, who has signed a four-year deal to become England's permanent boss, prepares to bring in his own coaching team.
"I should like to place on record my sincere thanks to The FA for the opportunity they gave me to work with the national team. It has been a great honour," Lee told the FA's official website.
"I should also like to thank the players and staff for their support during this period of my career and wish them all the very best for the future.
"In particular I wish Gareth [Southgate] and his new coaching team every success in the future."
Southgate has thanked Lee for his services during a difficult time but is adamant he needs to appoint his own staff to help move the team forward.
"I felt it was important for me to bring in my own support team and Sammy fully respected that," Southgate insisted.
"I was grateful with the way he helped to steady the ship throughout October and November and we wish him well for the future."
The FA have announced news on further appointments will be announced shortly with Chelsea coach Steve Holland expected to feature prominently in Southgate's plans.
