In 2002 they won the Scottish Amateur Cup at Hampden Park when they defeated Dumbarton Academy Former Pupils 4–2 in the final.

They retained the trophy the following year, beating Newmilns Vesuvius 1–0 in the final, again at Hampden Park.

In 2015, Harestanes won the Scottish Amateur Cup for a third time, which under new rules introduced that year meant they became the first ever winners of the trophy to qualify for the senior Scottish Cup.

They made their Scottish Cup debut in a preliminary round tie in August 2015, losing 3–0 to Girvan.

[1] The match was a home tie for Harestanes, but with Merklands being deemed unsuitable, it was played at Duncansfield Park, Kilsyth, in front of three hundred spectators.