Llandudno Junction FC was founded as Hotpoint FC in 1975, playing in the Old Colwyn and District Sunday League.
During the 1996–97 season, the team moved to Llanfairfechan’s Recreation Ground due to the limitations of the Victoria Drive ground. As a result, the team changed its name to Llanfairfechan Athletic.
In 1998, the club returned to Llandudno Junction, to their current ground at The Flyover, which had previously been the home of Crosville. The team changed its name again, to Llandudno Junction FC, for the 1999–2000 season.
In the 2008–09 season, the club won the Barritt Cup and had in their squad future Wolves striker Jake Cassidy.
In 2017, Junction was promoted to the Cymru Alliance, the highest level they had ever played at. However, they lasted only one season in the league before being relegated.
In 2018-19 they were again relegated, having finished bottom of Division 1 of the Welsh Alliance League.