Established in 2009 by school friends looking to play competitive football together, Flint Mountain began in the now defunct Clwyd League. In 2011, the club joined the North East Wales League as founding members after the Clwyd League was restructured and replaced. That season, despite finishing bottom of the table, they defied the odds by clinching the end of season Auxiliary Cup, the club's first piece of silverware.

Over the next few years the club took on a nomadic nature, as they moved between grounds in Flint, Connah’s Quay, Rhydymwyn, Sychdyn and Northop Hall. In 2019, Flint Mountain were crowned champions of the North East Wales League in an unbeaten league season, whilst also securing three cups in a quadruple winning season. That success, coupled with a move to Pant Newydd in Halkyn, saw the newly renamed Halkyn & Flint Mountain promoted to the Welsh National League Division One, where they finished sixth in a debut season blighted by poor weather and the early curtailment of the season due to the Coronavirus pandemic.

In 2021, following another league restructure, the club finished runners-up in the new North East Wales Premier Division and were promoted to the Ardal North West League. At the end of the season, the club returned to their home town of Flint after a ten year absence after agreeing to groundshare at the Essity Stadium, home of Flint Town United. The club also returned to its roots by changing its name back to Flint Mountain Football Club.

After a fourth placed finish in our debut campaign, this was followed by becoming champions of the Ardal North West League in our second season at Tier 3, as well as winning the North East Wales Football Association (NEWFA) Challenge Cup for the first time.

A third promotion in five years saw Mountain rise to the Cymru North for the first time, where a seventh place finish cemented their place in tier 2.