The club was previously called Bodedern Football Club and were playing in the Cymru Alliance up to the 2006–07 season, but resigned from the league on 16 October 2007 due to a shortage of players.[2] The club changed its name to Bodedern Athletic and took its reserves' place in the Gwynedd League.
In 2009–10 the club won promotion from the Gwynedd League as runners up. The following season the club won back to back promotions finishing as runners up in the Welsh Alliance League Division 2.
On 9 June 2022, it was announced that the club had been promoted to the tier 3 Ardal NW League for the 2022–23 season.[3] However the club folded in December 2022 and resigned from the league.[4]