Troon formed an Under-19 team in the summer of 2013 to be led by Head Coach Neil Duffy. The target for the Under-19 team was to provide a platform for young players to learn and grow before making the step up to compete for a place in the Junior side. A first season was very successful with two trophies being won, before the team lifted every single trophy they competed for in 2014–15. Captain Morgan Brown was subsequently signed up by Troon F.C. to make the step up alongside left-back Ben Wilson and midfielder Ross McCrea, whilst fellow midfielder Sean Ewart joined Whitletts Victoria. Manager Neil Duffy also stepped up to help out with the first team, before leaving only a few months later.
For season 2015–16 Troon F.C. will absorb last season’s Troon Thistle Under-17s as they make the step up to Under-19 level, under the tutelage of Derek Cowan & Henry McAvoy and in June 2017 Justin Brown was appointed Head Coach to oversee the transition for the new intake of players for the 2000 born players.