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Foundation

After the winding-up of Newry City F.C., discussions to form a new club began in December 2012. In February 2013, it was clarified that Newry City A.F.C. would be a new club and would not be liable for any debt owed by Newry City F.C. There were discussions for the club to join the Republic of Ireland's League of Ireland, however the Irish Football Association said that they would block any attempt for Newry City to join the League of Ireland. Newry City A.F.C. uses the old club's stadium, the Showgrounds, which is owned by Newry City F.C.'s season-ticket holders. This meant that it was not sold when Newry City F.C. was wound up.

Despite initial plans for the club to be named "Newry City 2012", Newry City A.F.C. was officially launched by former Newry Town player Ollie Ralph on 7 March 2013, and it was announced that they would seek to join the Irish Football Association, and play in the Intermediate B division of the Mid-Ulster Football League in the 2013–14 season. Northern Ireland manager Michael O'Neill was originally scheduled to take part in the club's launch, but was unable to attend.

Junior football from 2013

In July 2013, the club was accepted as a member of the Mid-Ulster Football League Intermediate B division for the 2013–14 season - the fifth tier of football in Northern Ireland. They won the division in their first season, gaining immediate promotion to Intermediate A (the fourth tier), which in turn they won in 2015–16 after two seasons, earning promotion to the NIFL Premier Intermediate League (the third tier). In their first season in their division, the club were runners up, qualifying for the NIFL Championship Play-Off. Over two legs, the team beat Armagh City 7–2 on aggregate to earn promotion to the NIFL Championship for the 2017–18 season, a third promotion in four years, and confirming the return of senior league football to the city for the first time since 2011.

Senior football from 2017

The club's rise was completed in the following season, as the runners-up spot in the 2017–18 Championship, and a 6–3 aggregate win over Carrick Rangers in the NIFL Premiership play-off saw the team reach the national top flight for the first time since its foundation, and top tier football return to the city for the first time since 2011. Relegated to the NIFL Championship the following season (2018–19), the club remained in the Championship during the COVID affected seasons 2019–20, and 2020–21, eventually earning promotion back to the Premiership the following season by winning the Championship title. The 2021–22 NIFL Championship was the club's first senior title since its formation.

The 2022–23 season saw the club secure a tenth-place finish, avoiding relegation in their maiden season back in the Premiership.

Post Darren Mullen Era

In 2023, manager Darren Mullen stood down, having been in charge since the clubs reformation in 2012, with Mullen's assistant Gary Boyle replacing him at the helm. The transition did not prove to be a successful one. With the club rooted to the foot of the NIFL Premiership table, Boyle resigned on 26 December 2023 following a 4–0 defeat to Glenavon.

On 2 January 2024, the club appointed former Warrenpoint Town and Cliftonville manager Barry Gray as Boyle's successor on a long term contract.

In April 2024, the clubs relegation was confirmed, following confirmation that Portadown had won the NIFL Championship, meaning Dundela, who were ineligible to be promoted, could not win the league.