Murty was twice placed in caretaker charge of the Ibrox club - firstly following the departure of Mark Warburton in February 2017 when he took charge of six matches before the appointment of Pedro Caixinha.
After Caixinha was sacked in October 2017, Murty was again placed in control of the first team before being appointed permanent manager until the end of the season, but was unable to prevent Celtic from winning a seventh consecutive title.
He returned to his role with the Under-20s following the appointment of Steven Gerrard in June 2018. He had been serving as Head of Elite Academy Development under Gerrard but his departure has been confirmed following the appointment of new head coach Giovanni Van Bronckhorst.
A club statement read: "Rangers FC thank Graeme for his outstanding service throughout his five years at the club, including when he stepped up to take on first-team responsibilities at the request of the board.
"Graeme has played a leading role in the development of our Academy players and practices, leading our development squad to success in the SPFL Reserve League and managing our first steps into the UEFA Youth League in 2019.
"We wish Graeme every success in his future career."
In total Murty took charge of 35 Rangers matches, winning 21, drawing three and losing 11.
Rangers sporting director Ross Wilson added: “Graeme is someone who has significantly contributed to the development of our Academy in recent times and for that I extend my personal thanks to him.
"As a club we also place on record our gratitude for Graeme’s support around our first-team a few years ago.
“Although it was before my time at the club I am aware of the dedication he showed to Rangers in a trying moment. We all wish Graeme and his family well for the next chapter in his coaching career.
"From our perspective, the role of Head of Elite Academy Development is integral to the on-going evolution and development of our academy that we have been working through and we have a clear plan for who and what will follow and we are excited about that.”
Craig Mullholland, Rangers' head of academy, added: “I would like to thank Graeme for his contribution to the positive evolution of our Academy during his time at the club.
"He had a sigificant influence on the development of many players and coaches and I know they would also like me to convey their thanks and wish him well in his next venture.”