Formed in May 1964 with assistance from the Glenrothes Development Corporation, the "Glens" played their first match against near neighbours Thornton Hibs in August of that year at their original Dovecot Park ground. A crowd of 5,400 attended a Scottish Junior Cup quarter-final tie against Shotts Bon Accord at  Dovecot Park during Glenrothes' run to the final in 1968.

The club moved to the purpose-built Warout Stadium in 1971, one of the larger grounds in Junior football, with room for around 5,000 spectators, 730 of whom can be seated. The record attendance for this ground is 5,600 against Cambuslang Rangers in another Junior Cup quarter-final tie in 1974.

Glenrothes' greatest success as a club came in 1975 when they won the Scottish Junior Cup, defeating Rutherglen Glencairn 1–0, in front of a crowd of 17,776 at Hampden Park. Glens had also been runners-up in 1968, losing after a replay to Johnstone Burgh with a combined attendance of 50,000 over the two ties, an impressive achievement given that they had only been formed a mere four years beforehand.