[16] After quickly gaining promotion to the First Division and consolidating their place under Maitland, in 2005 Hamilton brought in Billy Reid from Clyde to be the next manager, with MacDonald and other staff also previously having worked with him in that club's youth system.

[20][7][21] Relegation followed in 2011 and Reid departed two years later;[4] his successor Alex Neil, the club captain who spent a period as youth coach then player-manager,[8] put together another team featuring several more academy products which won promotion again in 2014, via the play-offs.

[33] In 2017, the Hamilton academy was one of eight across the country designated 'elite' status on the introduction of Project Brave,[16] an SFA initiative to concentrate the development of the best young players at a smaller number of clubs with high quality facilities and coaching than was previously the case.

[37] The also had to invest a large sum in a new artificial playing surface[38] after the existing one was voted the worst in Scotland,[39] had to cope with the death of serving community coach and former youth player Matthew Craig,[40] and suffered an arson attack on their stadium.

[48] Hamilton were eventually relegated from the Premiership in 2021[49][50] and then dropped down from the Scottish Championship in 2023, both necessitating cost-cutting measures across the club, although the decision was made to remain full-time and maintain funding for the youth academy.

[66] In the second round, the opponents were Denmark's FC Midtjylland Academy which produced Simon Kjær, Winston Reid, Jonas Lössl and Erik Sviatchenko, and whose senior team were the reigning national champions.

[67] In the return in Scotland, watched by a crowd of over 2,000 as in the previous round, Hamilton took the lead through Andrew Winter suggesting the possibility of a comeback, but then conceded an equaliser and away goal in the second half via a penalty converted by Tengstedt.

[71] Their exit appeared to be confirmed when Molde went ahead at New Douglas Park, but three goals from Ben Black (two penalties) and one from Paddy Meechan within the next hour brought the aggregate score level.

[72] Hamilton's main appeal to potential signings is the emphasis they place on developing players from within,[23][20] and the likelihood that those coming through will be more likely to be given opportunities to prove themselves than elsewhere,[24][74] as evidenced in both the 2016–17[75] and 2017–18 season when analysis by the CIES Football Observatory showed they were the leading club in the Scottish Premiership in terms of minutes on the field by homegrown players[76] (Celtic also scored well, although the majority of their contributions came from three regulars who are in the Scottish national squad – Tierney, Forrest and McGregor – rather than untried youngsters being thrown in).

[75] The club aim to maximise use of their facilities at New Douglas Park,[7] with the artificial surface not subject to the same wear as a grass pitch; it is therefore used by the senior and youth teams for both training and matches whenever possible.

[78] The head of the academy who coordinates a team of coaches across the age groups is George Cairns,[46] and the director of youth football (as well as the chairman from 2019, replacing Ronnie MacDonald)[79] is former first-team manager Allan Maitland.

Some of the club's earlier notable players also came through the youth setup, including three of the longest servants Rikki Ferguson, Stan Anderson and Jamie Fairlie, as well as John Brown who won 14 trophies at Rangers and Paul Hartley who appeared 25 times for Scotland.