In addition to their first team competing in the Scottish Premiership, Hamilton Academical F.C. also maintain a reserve team competing in the SPFL Reserve League, as well as further teams for younger age groups playing in competitions such as the Scottish Challenge Cup and the Scottish Youth Cup within the club's academy.
A reserve team was fielded for many years until the abandonment of the most recent league for those teams in 2009. An under-20 side took part in the SPFL Development League until it was disbanded in 2018.
Honours
Reserves
- Scottish 2nd XI Cup: 1933–34
- Scottish Reserve League (West): 1978–79, 1979–80, 1997–98
- Scottish Reserve League Cup: 1983–84, 2011–12
- SPFL Reserve League: 2019–20
Youth
- SPFL Development League: Runners-up 2015–16, 2016–17
- SPFL Under-17 League: Winners 2017–18
- SFL Under-19 League Cup: Winners 2012–13
- SFL Under-17 League Cup: Winners 2003–04
- SAFA Under-18 Cup: Winners 1991–92
- ^ Youth league running since 1993. Previously known as the Scottish Football League Youth Division, Scottish Premier under-18/under-19/under-20 League and SPFL under-20 League