Gresford Athletic won the Welsh National League East Division in the 1946/47 season. The next time the club won a league trophy was in 1962/63, when they won the Welsh National League Division Two. In 1969, Division Three was split into two sections, A and B, with Gresford Athletic Reserves winning the Welsh National League Division Three A title.

The club remained in the Welsh National League until the introduction of the Cymru Alliance in the 1990/91 season, when they became one of the founder members of the league. They remained in the Cymru Alliance for four seasons before being relegated back to the Welsh National League in 1994. During this four-year period, they reached the Cymru Alliance League Cup final, losing to a very strong Rhyl side.

Promotion was achieved in the 2000/01 season when they were once again champions of the Welsh National League Premier and, with the finances in place, the club’s Committee managed to upgrade the club's home ground, Clappers Lane, to Cymru Alliance standards. In the same season, they were also beaten in the FAW Trophy final.

Alan Jones, nicknamed Sammy, left his role as First Team Manager of Gresford Athletic in 2008, after over 20 years of being at the club, earning seven trophies and cementing his legendary status within the club. He was replaced by Sam Ainge, who was promoted from Gresford Athletic Reserves.

Upon the re-structure of football in Wales, they re-entered the Welsh National League Premier in the 2010/11 season following nine seasons in the Cymru Alliance. This proved to be a difficult season for the club, with them finishing in the bottom four. However, the following three seasons saw them steadily move up the league table.

The summer of 2014 saw a new management team and committee introduced at the club, which brought in a number of new players in and the emphasis both on and off the pitch being on achieving promotion to the Cymru Alliance. Eddie Maurice-Jones was appointed as First Team Manager and Julian Davies became the club’s Chairman, replacing Rob Ratcliffe.

A 24-match unbeaten run saw Gresford Athletic maintain a control on the league, whilst also seeing a successful run in the Welsh Cup, Welsh Trophy and Welsh National League Premier Cup competitions and it was January before they finally lost a game. However, the Welsh National League Premier title was not clinched until the final game of the season, by which time the work had been completed behind the scenes, with promotion to the Cymru Alliance having already been confirmed.

The 2015/16 season saw Gresford Athletic claim their highest ever finish in the second tier of Welsh football, when they finished the season in sixth place.

In the 2016/17 season, Gresford Athletic Reserves Manager Steve Halliwell was appointed as First Team Manager, following the departure of Eddie Maurice-Jones to Denbigh Town. He led the club to win the NEWFA Challenge Cup for the third time in their history. The final was played against Queens Park, with Gresford Athletic deservedly winning 3-2 at full time.

Two seasons later, Gresford Athletic then went onto be runners up in the NEWFA Challenge Cup, losing 4-1 to Cefn Druids in the 2018/19 final.

Ahead of the formation of the new Cymru North for the 2019/20 season, replacing the previous Cymru Alliance, Gresford Athletic underwent a restructure on the coaching staff. The club appointed their first ever Director of Football in Steve Halliwell, leaving his role as First Team Manager, within the new-look coaching staff. Richard Capper was appointed First Team Manager.

Gresford Athletic finished 11th in the first season of the Cymru North, which was cut short due to the COVID-19 pandemic, and have been members of the Cymru North from the 2020/21 season onwards.

Eddie Maurice-Jones returned to the club for his second spell as First Team Manager in June 2020, with former Gresford Athletic goalkeeper Jonathan Hill-Dunt joining him as First Team Assistant Manager in 2021.

The 2022/23 season saw a big change for the Gresford Athletic First Team, as they agreed a multi-year deal to see the team move from Clappers Lane to The Rock, groundsharing with Cefn Druids. The move came due to the increasing Tier 2 criteria from the Football Assoiciation of Wales, meaning that Clappers Lane would prove difficult to be up to the minimum standard to host games in the Cymru North and could result in a rejection of the club’s Tier 2 license for the 2023/24 season. Despite the move, the club’s Reserves remained at Clappers Lane, keeping the club’s feet within the village of Gresford.

The final Gresford Athletic First Team home game played at Clappers Lane was a 1-0 win against Ruthin Town in February 2023, with their first home game played at The Rock coming in March 2023, when they drew 1-1 with Prestatyn Town.