 Brogan and Clark took charge of East Kilbride Thistle in November 1999, with Brogan assuming full control when Clark left to join the Celtic youth set-up in 2002.With East Kilbride, he won the Sectional League Cup in 2002 and promotion from Central District First Division in 2006.Brogan took over as the manager of Yoker Athletic in 2008, leading the club to two successive promotions.