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Scottish Cup

The Spartans' most successful Scottish Cup run was in 2003–04, when they defeated Buckie Thistle 6–1 in front of a crowd of 450 in Edinburgh in the first round, before defeating Alloa Athletic 5–3 in a replay (the first game had been drawn 3–3) in Edinburgh in the second round. They then defeated Arbroath (who had been in the SFL First Division only the year before) 4–1 at Gayfield Park in the third round, before being beaten 4–0 at home by Scottish Premier League team Livingston in front of a full house of 3,000 fans at City Park.

Two seasons later in 2005–06, Spartans defeated Berwick Rangers, Lossiemouth and Queen's Park in the first three rounds of the Scottish Cup. They drew 0–0 with First Division side St Mirren in the last sixteen in front of 3,326 fans at City Park, earning a replay at Love Street, where they lost 3–0.

In the 2008–09 Scottish Cup, Spartans' cup run sent them to Pollok, winning through a replay, they then beat Annan Athletic 2–1. In the next round they beat Elgin City 2–1, before being knocked out by Airdrie United in the fourth round.

Spartans, along with four other clubs, submitted an application for entry into the Scottish Football League following Gretna relinquishing their league status on 3 June 2008. Spartans lost out to Annan Athletic.

In November 2008, Spartans moved to a new purpose-built home at Ainslie Park, situated 500 yards from City Park in the Crewe Toll district of Edinburgh. The new facility includes a 504-seater stand and floodlights surrounding the main stadium pitch and an adjacent, full size artificial pitch with floodlights. Ainslie Park is now used daily by youth and adult Spartans teams, along with the general public. The club also won the league title this season.

In the 2009–10 season, Spartans won the quadruple, consisting of the East of Scotland Premier Division, the SFA South Challenge Cup, the King Cup and the League Cup. The 2009–10 league title gave Spartans back to back title wins for the first time since 2005.

During the 2010–11 season, Spartans won their third league title in a row. The next season they lost the league title on goal difference to Stirling University, while in the 2012–13 season, they finished third in the league.

Lowland League

Spartans joined the newly formed Lowland Football League for the 2013–14 season, winning the inaugural title. They finished as runners-up in 2015–16 and won the League Cup a year later, before becoming Lowland League champions for a second time in 2017–18. This allowed Spartans to take part in the Pyramid play-off, however they lost 5–2 on aggregate to Cove Rangers.

The club progressed to the fifth round (last 16) of the 2014–15 Scottish Cup, defeating Clyde and Morton en route.

In the fifth round of the competition, Spartans forced a replay with Berwick Rangers on 7 February 2015, thanks to an injury time equaliser from Ally MacKinnon to level the tie at 1–1, the game being played in front of 2504 supporters at Ainslie Park.

In the 2022–23 season, Spartans won the Lowland League title for a third time. During that season's Pyramid play-offs they defeated Highland League champions Brechin City 4–3 on penalties before defeating Albion Rovers 2–1 on aggregate in the final to progress to Scottish League Two.