In his early days he played for junior side Bonnyrigg Rose Athletic, during which time he played for a Scotland amateur team against England at Middlesbrough. Fowler was one of three players brought down from Scotland to, along with Sammy McLeod and Bobby Hill from Easthouses Lily, by manager Benny Fenton in 1955. Astute purchases, all three gave lengthy service to the club
Fowler made his debut along with Hill on 20 August 1955 in a goalless draw away to Exeter City.
Initially an inside left, he switched to left back later that season. Fowler still holds sixth place in Colchester"s all-time list of long serving players and fifth on the League appearances list and made the number 3 shirt his own for the majority of his career, being an integral part of the promotion sides of 1962 and 1966.
Between 1956–1963 Fowler missed only eight matches, becoming known as "Mr Reliable". He was an ever-present during the 1957-1958, 1959-1960, 1961-1962 and 1962-1963 seasons and only missed one game during 1960-1961.
Although he left the club at the end of the 1965-1966 season, Fowler returned briefly for three games during 1967-1968, his final appearance occurring on November 13, 1967 at home to Barrow.
Retirement and death After leaving, Fowlern became player-manager at Heybridge Swifts. Playing against Layer Fox, Fowler collapsed and died, aged 42. This is played for each season by teams in the Colchester & District Sunday League.
The cup has since been re-named The Fowler Memorial cup in memory of John and Scott, who has also died.
He was also a regular member of Peter Wright"s Ex-Colchester United XI.