The ex-Selkirk manager was appointed on a part-time basis to create and lead the club’s development squad with the remit of bringing ‘local players into the first team environment over time’.
Having worked at other successful youth academies in Scotland including Hearts and Hamilton, the coach was primarily working alongside Holt in his role.
At the AGM in December, Fergus updated supporters on the progress of the Under 18’s and 16’s sides that he was in charge of saying: “We want to find the next Craig Sibbald-type player who will grasp a chance in the first team and rise to the challenge and claim a starting spot.
"That has to be the goal for us as a club, to bring in the best local talent and give them the chance to excel at this great football club.”
He added: “Both teams are playing elite level sides and are improving each week.”
Fergus leaves in the wake of the club’s forthcoming review of football operations, with CEO Jamie Swinney currently overseeing youth development. Head coach Martin Rennie has taken on Gary Holt’s duties for the time being except this specific area.
It is expected that an appointment to replace Fergus will be announced imminently.