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The original Edinburgh City was founded in 1928. The club adopted amateur status, with the aim of becoming the Edinburgh equivalent of Queen's Park. Edinburgh City joined the Scottish Football League in 1931. The club played in the Lothian Amateur League during the Second World War and were only admitted to the C Division in 1946, by then the club had adopted professional status. After three more years of struggle, the club left the Scottish Football League in 1949. It switched to junior status and played in the Edinburgh & District Junior League. The club ceased activity completely in 1955, when the local council refused to renew its lease on its home ground, City Park.

A club called Postal United F.C. was founded in 1966 and joined the East of Scotland League. Their best league finish was third in 1985–86, having won the Qualifying Cup in 1982–83 and King Cup in 1984–85.

The Edinburgh City Football Club Ltd., which had continued trading as a social club since the football club stopped playing, gave their approval in 1986 for Postal United to use the Edinburgh City F.C. name. The club has participated in the Scottish Cup since the mid-1990s, when it became a full member of the Scottish Football Association. In the 1997–98 Scottish Cup they defeated SFL club, East Stirlingshire, before losing 7–2 to Dunfermline Athletic, then of the Premier Division.

The club applied to join the Scottish Football League in 2002, after Airdrieonians had gone bankrupt, but Gretna won the vote instead. Edinburgh City applied again following Gretna's liquidation in 2008, but this time lost out to Annan Athletic.

Edinburgh City won the East of Scotland Football League Premier Division title for the first time in the 2005–06 season and became members of the new Lowland League in 2013. The club won the Lowland League title in 2014–15 and 2015–16. They then gained promotion to the Scottish Professional Football League by defeating East Stirlingshire in a play-off with a penalty four minutes from time by Dougie Gair. The victory also meant that it was the first time that a non-league club had been promoted to the professional league. The club finished in seventh place during their first Scottish League Two season of 2016–17. They avoided the relegation play-offs in 2018, finishing eight points ahead of bottom placed Cowdenbeath, and fared better in 2018–19, finishing third and qualifying for the League One promotion play-offs; however, they were knocked out by Clyde in the play-off semi-finals, losing 4–0 over two legs. Edinburgh City sat second in the table after 27 games when the truncated 2019–20 season was brought to an early finish in April 2020.

Despite finishing 4th in the 2021–22 season, Edinburgh City navigated through the League One play-offs and earned promotion to the Scottish League One, the 3rd tier in Scottish football, for the first time in their history.

In June 2022 the club changed their name to FC Edinburgh, as they no longer felt the 1986 permission from the Edinburgh City social club to use the name was sufficient, and wished to own their own name outright. When the social club refused to surrender the name, the football club changed to "Football Club of Edinburgh". The club clarified in October 2022 that it should be known as Edinburgh, rather than its full name of FC Edinburgh.

In June 2023 it was announced that ownership would be transferred from Tom Tracy to a fan based consortium led by John Dickson. It was also announced that the club would revert back to being called Edinburgh City pending SFA approval. Later in June 2023 SFA approval was confirmed.

City were relegated to League Two after a 5–2 defeat to Alloa Athletic on 16 March 2024.