Young replaced Chris McCart in the Fir Park role five years ago, following the latter's departure for Celtic, and has twice had spells as caretaker manager.
He will oversee the expansion of United's youth academy, and will be actively involved in the setting up of academies throughout Europe on behalf of the Sky Bet League One club.
Motherwell chief executive Leeann Dempster said: "We would like to put on record our acknowledgement and thanks to Gordon for all his hard work, particularly his two stints as interim manager of the first team.
"We are obviously sad to see Gordon go, however this is a new chapter in his career and also an exciting opportunity for the club to appoint a successor.
"I plan to meet with a few candidates over the course of the next 10 days or so."
The former Rangers and Charlton striker Jonatan Johansson, who is currently in charge of Motherwell's U20 set-up, is one possible contender for the vacancy.