Glantraeth Football Club was formed in 1984 and set up its base on land adjacent to the Glantraeth Restaurant made available by landowner Mr Iolo Owen. The club entered the Anglesey League in Division 2, 1985/86 saw the team finish as Runners up under manager Robin Evans, and the following season the honour of an appearance in their first Cup final the (Dargie cup) and promotion to Division 1 of the Anglesey League.

Further honours followed as the Glan were Runners up in the Anglesey League in 1987/88, a League title win in 1989/90 saw the club gain promotion to the Gwynedd Football League, their first step along the Pyramid system within Wales, as well that same season the team reached the finals of the Elias Cup and also the N.W.C.F.A Junior Cup.

Over the next five years the club enjoyed a good deal of success winning a succession of trophies, in 1992/93 they were Gwynedd Cup finalists and Eryri Shield winners, 1993/94 they captured the Gwynedd League championship, and subsequent promotion was achieved to the Welsh Alliance League, also that same season they won the Gwynedd cup and appeared as finalists in the Eryri Shield, in 1994/95 they were Runners up in the Barritt cup and 1995/96 they became winners of the Alves cup.

In 1996/97 under manager Alan 'Ali' Jones Glantraeth were crowned as Champions of the Welsh Alliance League gaining promotion to the equivalent of Division 2 of Welsh football the Cymru Alliance League, at this point a lot of work was put in by the small band of dedicated committee members to ensure the promotion was rubber stamped at the A.G.M of the League. A stand had to be built alterations to the changing rooms and the drainage system also needed looking at.

In 1999/2000 under Manager Mike Owen the team were finalists of the Premier cup in North Wales the (N.W.C.F.A.Challenge Cup). Season 2000/2001 was the pinnacle as the club became Runners up in the Cymru Alliance League, leading to speculation of possible promotion to the ultimate League of Wales, but this did not materialise.

In season 2002/2003 The Club re formed and with the blessing of the F.A. of Wales, they entered the Welsh Alliance League. Bob Brodie and assistants Maldwyn Hughes and Ray White, assembled a squad that on the very final day of the season won the League title by one point over arch rivals Bodedern, they were also losing finalists in the Cookson Cup and Barritt Cup.

Season 2003/2004 saw a change of management as Paul Whelan took charge, assisted by Emrys Jones. The introduction of several new players saw the team achieve a creditable fourth position in the League and also a run in the Welsh Cup to the Quarter Final stage against Total Network Solutions.

Season 2004/2005 Emrys Jones stood down and Peter McCann came in to assist Paul Whelan. The club further improved on the previous season finishing runners up in the Cymru Alliance for a second time.

The Club had their most successfull season ever in 2005/06 becoming the first Anglesey based club to do the Double, winning the Cymru Alliance Championship and also the Cymru Alliance League Challenge Cup (Top picture). The club could not accept promotion as the ground at Cae Trefdraeth did not meet the requirements of the higher league.

It proved a hard act to follow in 2006/07 season although Glantraeth finished in a respectable fifth position.

At the end of 2007/08 season manager Paul Whelan moved to Welsh Premier League Porthmadog and former Bodedern manager Kev Hughes was appointed as his replacement. After only five games the club and manager parted company and Gareth Roberts took charge. In what was proving a difficult season he resigned in January 2009 and Emyr Rowlands accepted the role of acting player manager until the end of the season.

In the summer of 2009 the club made the shock decision to resign from the Cymru Alliance and withdraw from playing football for a season.

During the club's one year absence from football a great deal of work was carried out on the ground including concrete hardstanding, new spectator barriers, a new toilet block and the ground was fenced off from surrounding farmland. The FA of Wales made the decision that the club would resume playing in the Gwynedd League. Kev O'Neill and Chris Roberts were appointed managers for 2010/11 season.

Glantraeth marked their return to football in 2010/11 with one of the most incredible seasons in the club's history, gaining promotion to the Welsh Alliance as Gwynedd League Runners-up and winning four cup finals in a 14 day period in May that included the prestigious North Wales Coast FA Intermediate Cup.

Season 2011/12 saw Glantraeth again promoted as Welsh Alliance Division Two Champions and go on to complete the double by winning the League Cup at Caernarfon Town FC against Llanberis. The last game of the season saw Glantraeth meet top Welsh Premier League side Bangor City on their own Nantporth ground in the final of the North Wales Coast FA Challenge Cup. eventually losing 4-1 to their illustrious opponents.

Following promotion to Division One 2012/13 proved a season of transition and consolidation under manager Chris Roberts, the team finishing mid-table. More work was carried out on the ground with the main stand refurbished including the fitting of new tip- up seats, improving of drainage at the canteen end and the purchase and fitting of new Stadium style goals.

Former player Warren Gibbs was appointed manager for 2014/15 season and the club had their best season in the FAW Trophy after reaching the semi-finals. A season later Glantraeth won the Cookson Cup for the first time beating Llanberis 3-0 at Bangor City FC as well as reaching the final of the Mawddach Challenge Cup.