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The club was formed in 2013, initially as a group of friends who drank at the Bruno's Bar & Restaurant (a bar in Gibraltar). In its first two seasons, the club achieved respectable mid-table finishes in the Gibraltar Second Division. Mick Embleton was appointed the first manager of the team and was instrumental in the initial setting up, organising and managing of the squad.

With the introduction of Chestertons, a Gibraltarian real estate agent, as the sponsor in 2015–16, the intent grew more serious, with moves to professionalise the club and establish a fanbase with the introduction of matchday programs and incentives for fans who attended games.^[] The club finished fourth in that season and were the runners-up in the Second Division Cup, losing in extra time to Second Division champions Europa Point.

In October 2016, the club appointed Davie Wilson as manager, who has previously been assistant-manager the Gibraltar national football team and had recently departed Gibraltar Premier Division side Lions. The club enjoyed a dominant start to the campaign, however a faltering winter saw them embroiled in a title race with the resurgent Gibraltar Phoenix. Ending the season in second place, they entered the play-off with Manchester 62, who finished 9th in the 2016–17 Gibraltar Premier Division. However, a 3–1 defeat ensured that The Magpies remained in the Second Division for the following season.

In August 2017, the club announced a new sponsorship deal with GVC Holdings. The side finished 3rd in the league that season, however, in May 2019 they completed a league and cup double, securing the Second Division title while also winning the Second Division Cup. After the season concluded, the club announced that former Watford chairman and British Olympian Haig Oundjian had purchased a stake in the club and become co-chairman with Louis Perry.

The appointment of Nathan Rooney midway through the 2021–22 season saw a significant upturn in Magpies' fortunes in the league, with a 4rd place finish and a first Rock Cup final. The next season, along with an overhaul of the club's image, saw more improvement, with a 3rd place finish and victory in the 2022–23 Rock Cup. However, on 17 May 2023, Rooney announced his departure from the club.