[1] In 1996, McGlynn was invited to assist with coaching the youth sides at Heart of Midlothian by newly appointed manager Jim Jefferies, initially on a part-time basis.
[5] Rovers' second season in the Scottish Second Division ended in disappointment, finishing third and beaten in the promotion play-off semi-finals against Stirling Albion.
[10] McGlynn led Raith to a comfortable seventh place[11] and took the club into their first Scottish Cup semi-final for 47 years,[12] beating Peterhead,[13] Airdrie,[14] Aberdeen[15] and Dundee.
[9] Despite losing out to Fife derby rivals Dunfermline Athletic in the final weeks of the season,[9] McGlynn won the PFA Scotland Manager of the Year award.
[18] With the restricted budget imposed by the club's financial situation he was only able to bring in two new signings and he put his faith in many young players coming through the youth ranks.
Hearts started the SPL season badly under McGlynn, with only one win in the first six games, and lost in the Europa League play-off against Liverpool 2–1 on aggregate, drawing at Anfield.
[26] After overseeing good results that improved Livingston's league position, McGlynn agreed an extended rolling contract with the club.