Hayes Football Club was founded in 1909 when Eileen Shackle, the teenage daughter of a wealthy land agent, encouraged the local youngsters to form a football team. The team was originally known as Botwell Mission, after the mission church that was built in memory of her grandfather, and that still stands today as part of the Hayes Library in Golden Crescent.

The young club won its first trophy, the Middlesex Minor Cup, in 1912, against another church-based team, Southall Church Lads Brigade. The club entered its first league, the Uxbridge & District, in 1912, winning it at the first attempt. At the onset of the First World War every member of the club volunteered for war service. The club's first captain in 1909, Albert Knight, one of the seven footballing Knight brothers, was killed at the Somme, and William Vaughan, who was in The Gordon Highlanders, was killed in action in 1917.

In 1919 Botwell Mission entered senior football, playing in the Great Western Suburban League. At the end of the season the club won the Middlesex Senior Cup at the first attempt, beating Southall at Brentford. Next season, the club both retained the county cup and won the league championship for the first of four consecutive seasons, after which it was invited to join the Spartan League. Botwell Mission finished their first season at this level behind champions Maidenhead United, but won the title in 1927-8.

At the end of the 1928-29 season the club changed its name to Hayes Football Club. The effect was immediate - in 1930, Hayes was elected to the Athenian League. In its first season at this level, it reached the Amateur Cup Final, played at Highbury. This was notable for the fact that the club had started at the 1st qualifying round stage, and had played all its nine matches away from home, travelling an estimated 1,500 miles to places as diverse as Wisbech, Trowbridge, Stalybridge (where Northern Nomads played), and York for a semi-final against Bishop Auckland. The final was lost to Wycombe Wanderers by
one goal to nil.

Hayes were runners-up for the Athenian League championship in 1931-32 and again in 1949-50. The record attendance at Church Road was set in February 1951 when 15,370 saw the Amateur Cup tie with Bromley. In 1956-57 season the Athenian League title was won on goal average over Finchley and the semi-final of the Amateur Cup was reached, losing to Bishop Auckland before a crowd of 32,000 at St James Park, Newcastle.

Some lean years followed through the sixties until the club was invited to join the Isthmian League in 1971. Although its league form was indifferent, some good FA Cup encounters occurred, the first giant-killing coming with a home win over Bristol Rovers in the 1972-73 season, before going down to Reading in the next round after a replay. Other FA Cup successes came against Cardiff City, in a replay at Brentford's Griffin Park, and against Fulham at Craven Cottage. During the period 1987-2002, Hayes reached the 1st round proper of the competition on 13 occasions, and overall have four times reached round 2.

In 1996, Hayes reached the pinnacle of non-league football by winning the Isthmian League championship by one goal in a nail-biting finale which also involved Enfield, Yeovil Town and Boreham Wood. The club maintained a presence at this level for six seasons, including finishing in 3rd place in 1998-9, before suffering relegation for the first time in 2002. Having spent a couple of seasons back in the Isthmian League Premier Division, they became one of the sides who earned a place in the new Conference South league.

Famous players to have worn the red and white stripes include Freddie Knight, Leslie Smith, Hayes' first full international, Len Townsend, George Wilkins, Johnny Gregory, Jimmy Bloomfield, amateur internationals Frank Bridges, Ron Gadsden, Jack Rawlings and Les Champelovier, Derek Neate, Robin Friday, Cyrille Regis, Les Ferdinand and most recently Jason Roberts.