Merthyr Saints remained in Welsh League Division Two for ten successive seasons with the highest finishing place of fifth in 2003/04.

Currently Merthyr Saints best performance in the FAW Welsh Cup came during the 2011–12 season when progressing to the Third Round before losing 6–0 to Cymru Premier League side Bala Town at the ICI Rifle ground.

In August 2022, the club announced the appointment of Jordan Davies as Merthyr Saints first team Manager.

A seven-year stay in the South Wales Alliance League Premier Division came to an end in 2022–23 after a difficult season that included a nine-point deduction.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.