Established in 2009 by school friends looking to play competitive football together, Flint Mountain Football Club began in the now defunct Clwyd League, finishing bottom of the table in their first season with just one win and four points to their name. In 2011, the club joined the North East Wales League as founding members, after the Clwyd League was disbanded. That season, despite finishing bottom of the table again, 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 2022, the club finished runners-up in the 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 their roots by changing it's name back to Flint Mountain Football Club. A fourth place finish in our debut campaign at tier 3 now sees us look to build upon that ahead of the new season.