The 49-year-old has followed in the footsteps of assistant manager Mike Phelan and goalkeeping coach Eric Steele in leaving the club since Alex Ferguson's retirement
The Dutchman departs Old Trafford after serving 12 years on the coaching staff, which was interrupted briefly in 2006 for an ill-fated six month spell in charge of Danish club Brondby.
Meulensteen played an integral role in Sir Alex Ferguson's success over the last decade, but had been poised to leave the club ever since the Scot's retirement after seeing assistant manager Mike Phelan and goalkeeping coach Eric Steele depart following David Moyes' arrival.
Executive vice chairman Ed Woodward told the club's official website: "I'd like to thank Rene for his contribution to the club, particularly since he returned to Old Trafford in 2007.
"He has been first-team coach for five years and in that time has given great assistance to Sir Alex Ferguson and Mick Phelan in keeping the team at the top of the game not only in this country but in Europe as well.
"On behalf of everyone at United, I wish him well for the future."
Rene Meulensteen said: "I would like to thank Sir Alex Ferguson, the owners, all colleagues, players and fans who made my time at Manchester United very special and one I will never forget. I wish everyone at this great football club all the best."
Meulensteen originally arrived at Old Trafford from Qatari club Al Sadd as "skills development coach" in 2001, coaching all of the youngsters from age 9 to 21, before earning a promotion to reserve team manager following Ricky Sbragia's departure in 2005.
After leaving to take over at Brondby, he returned to the club in early 2007 and was appointed first-team coach when Carlos Queiroz's departure to manage Portugal led to Mike Phelan's promotion to assistant manager.
During his second spell at Old Trafford the club won four Premier League titles, two Capital One Cups and a Champions League in 2008.