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The present Elgin City club was formed on 10 August 1893 by the amalgamation of two Elgin sides, Rovers (Formed 1887) and Vale of Lossie (Founded 1888). However the name Elgin City was used by two clubs prior to this. The first was formed in October 1879, but lasted for only a short time. The second Elgin City was formed in October 1884 and lasted until early 1887.

The present club's first major honour came in the 1898–99 season when they became the first team outside Inverness to win the North of Scotland Cup, beating Clachnacuddin 2–1. However, they failed to record any more success aside from the Elgin District Cup until 1924 when they again won the North of Scotland Cup a second time. Since then they have won honours with relative frequency.

In 1968 the club reached the quarter-finals of the Scottish Cup, the furthest into the tournament that a Highland League club has ever progressed.

The club was granted league status in 2000 when the SPL was expanded to twelve clubs leaving two places to be filled. Peterhead joined them in the Third Division from the Highland League. Since joining the SFL, Elgin have struggled with consistency, and to this date have neither been promoted or relegated, but in season 2003–04 they recaptured the North of Scotland Cup.

In December 2005, assistant manager Kenny Black saw a takeover bid thwarted at the eleventh hour. Many fans saw his bid as the best chance to move upward through the leagues, but a controversial sale of shares in the club meant Black's bid was defeated. David Robertson, manager at the time, also chose to leave the club. Former Lossiemouth manager Graham Tatters was subsequently named as Elgin's new chairman. Club captain at the time Jamie McKenzie was appointed caretaker manager and a run of good results was rewarded with the Manager of the Month award for December 2005; at the time he was the youngest serving manager in the UK.

Early in 2006, former Aberdeen, Ross County and Scotland international, Brian Irvine was appointed manager. However, following a very poor start to the 2006–07 season, he left the club despite having forged a good relationship with the fans.

After a brief spell under interim manager Graham Tatters (during which they lost to Highland League Deveronvale in the Scottish Cup Third round), former Clachnacuddin manager Robbie Williamson was appointed in January 2007. Williamson quit on 20 December 2008, before a game with Berwick Rangers. He left the team bottom of the Third Division after just two wins from 15 matches.

On 23 January 2009, former player of Everton, Norwich City, Dundee, Dunfermline Athletic and Kilmarnock, Ross Jack was named as the club's new manager, signing a three-and-a-half-year-contract. He was a former player-manager of Montrose and former assistant coach at Ross County. On 5 January 2013, Elgin City became the first club to take a point from Rangers at Ibrox in the season, with the game finishing 1–1. Ross Jack left the club on 22 January 2014 after five years in charge, with the club lying in second bottom position of the division. In his time at the club, the high point was reaching the divisional play-offs at the end of season 2011–12.

Former player and assistant manager Barry Wilson was appointed as manager on 28 January 2014 and announced his intention to have a squad of north-based players. Barry Wilson resigned as manager on 17 November 2014 and was replaced by Jim Weir 10 days later. On 30 April 2016, they sealed the runners up spot in Scottish League Two and entered the promotion Play-offs. However, they lost 5–1 on aggregate to Clyde and remained in League Two. The club finished fifth in 2017, missing out on a play off spot by one point. 2018 saw another mid-table finish, as the club ended the campaign in sixth place on 49 points. In 2019, the club finished in eighth place, 24 points clear of the playoff spot.