The first Horsham Football Club was founded in 1871, though its existence largely depended upon enough players being available to form a side. In 1881 the club was firmly re-established, playing its first game against Dorking, and, in September 1882, helped found the Sussex County Football Association, with club official A. R. Bostock becoming one of three original Vice Presidents. Horsham became founder members of the West Sussex Senior League in 1896, winning the championship in 1899-00, 1900-01 and 1901-02, and claiming the Royal Irish Rifles Cup in 1900 by defeating the champions of the East Sussex Senior League, Hastings. After having played at both Hurst Park and Springfield Park, the club secured Queen Street as its permanent home in 1904, but some lean form over the ensuing years saw Horsham overlooked when the Sussex County League was created in 1920. The club eventually became members of that competition after winning the West Sussex Senior League for the fourth time in 1925-26.

This was a golden age for the club and the County League was won in 1932,1933, 1935, 1936, 1937 and 1938, regularly scoring over one hundred goals a season. The Sussex RUR Cup was taken in 1931, 1932, 1934, 1935, 1936, 1937 and 1938, and the Sussex Senior Cup in 1934 and 1939. After the break brought on by hostilities, Horsham won the first post-war title in 1947, the RUR Cup in 1946, 1949 and 1951, and the Sussex Senior Cup in 1950.

In 1947-48 Horsham reached the First Round Proper of the FA Cup for the first time, taking a first minute lead against Tommy Lawton's Notts County, before losing 9-1. For many years Horsham had been looking to test themselves at a higher level but had seen their annual applications to join the Athenian League come to nothing. In 1951 the club changed tack and successfully applied to become members of the Metropolitan League. This was a league that included the 'A' sides of top Football League clubs, the reserve sides of 'professional' non-league clubs and a few amateur teams. Despite some people insisting the Sussex club could not compete at such a level, Horsham answered their critics in the best possible way by winning the championship at the first attempt. However, over the years the league became stronger and stronger and eventually the amateur clubs struggled to make any impact at all. Having decided to quit the league in 1956-57, Horsham finished that season at the foot of the table. During this spell the Senior Cup was won for the fourth time in 1953-54 when Whitehawk & Manor Farm were beaten 1-0 at Brighton's Goldstone Ground. The RUR Cup was also won in 1952 and (for the last time) in 1957. Having decided to quit the league in 1956-57, Horsham finished that season at the foot of the table. In 1957 the club joined the amateur Corinthian League and began a period of consistent progress, finishing thirteenth, ninth, eighth and fifth before their best ever season in 1961-62 when third place was achieved.

Following a mass exodus of players, a young, local  team then finished twelfth in 1962-63 after which the league merged with the Delphian and Athenian Leagues to form the new three division Athenian League. The Corinthian League became the new Division One and Horsham finished thirteenth in 1963-64 and fourth in 1964-65 before a strong team consistently underachieved in 1965-66, finishing in fifteenth place and becoming the first Horsham side ever to be relegated. Under coach Pat Tobin, Horsham rebuilt their team in an effort to fight their way back to Division One and this reaped dividends in 1966-67 when the club once again reached the First Round Proper of the FA Cup when Swindon Town made the trip to Queen Street and emerged 3-0 victors in front of an 8,000 record crowd. Despite this achievement, this was a frustrating period of near misses for the club. In the league, promotion was just out of reach as the team finished third, third and fifth - and to make matters worse Horsham fell to three consecutive defeats in the final of the Sussex Senior Cup. The club (nicknamed the Hornets by their supporters in a popular competition in the 1968-69 season) appointed former Eastbourne United boss Roy Osborne as their new manager and the change brought immediate success, with the Division Two championship being won in 1969-70, and the Division One championship followed in 1972-73. The Sussex Senior Cup was then won again in 1972 when Whitehawk were defeated 2-1, again, at the Goldstone Ground.

Instead of taking their place in the Athenian League Premier Division, Horsham became members of the Isthmian League when that competition expanded to two divisions in 1973-74. The club finished eighth in its first season, and rounded the season off in style by once again winning the Sussex Senior Cup, defeating Worthing 2-1 in a competitive final. Another eighth place finish was secured in 1974-75 before Osborne left the club, with Tony Elkins-Green taking over the reins. Though Horsham finished only 11th in 1975-76, the Sussex Senior Cup was won again with another 2-1 win, this time over Hastings United. 1976-77 saw the Hornets have their best Isthmian season, with a sixth place finish, though 1977-78 was a poor year in which the team finished sixteenth, with Elkins-Green departing in September to be replaced by popular former player Tex Wiltshire. The highlight of the year was a first ever win in the Sussex Floodlight Cup when Worthing were defeated in the Final. In 1978-79 Horsham made a concerted bid for promotion, though money problems before the end of the season did not help the final push and the team eventually finished fifth, the club's highest ever position. However, the club's troubles were far worse than many had realised and only the dedicated work of chairman Frank King saw the club saved from bankruptcy and dissolution. A young, amateur team finished bottom of Division One in 1979-80 and the club was relegated to the new Division Two. Battling against their financial problems, the club endured some dark times under numerous managers in the 1980s, finishing bottom of the league in 1983-84 (though only after being deducted two points for fielding an unregistered player).

Horsham finished bottom of Division Two South in 1989-90 but a successful relegation play-off against Letchworth Garden City maintained the club's Isthmian status. Progress was made under the management of Peter Evans from 1990 during which time the club reached the final qualifying round of the FA Cup only to lose to neighbours Crawley Town after a replay, though under his replacement, John Yems, Horsham once again propped up the entire league in 1993-94. This led to the appointment of former captain Mark Dunk as manager and he led his side to the Division Three championship in 1995-96. After narrowly missing out on a second successive promotion, Dunk departed in 1997 with the club enduring three years of lower mid-table obscurity under Russell Mason and Nick Coombes before former Crawley Town boss John Maggs took over as manager in January 2000. After taking a struggling side out of the relegation zone in 1999-00, the following season a seventh place finish was achieved. Horsham then finished runners-up in Division Two in 2001-02, rounding off a successful campaign by beating Crawley Town to win the Sussex Floodlight Cup for the second time. Following the league re-organisation, Horsham found themselves in Division One South in 2002-03, finishing eighth. 2003-04 was a year of struggle as teams competed to win places in the newly restructured non-league pyramid and Horsham finished fifteenth, thus finding themselves in Division One for 2004-05. That season again saw a strong promotion charge fade away with Horsham finishing third and losing a promotion play-off final to Bromley at Queen Street by 3-1.

Promotion to the Premier Division was finally achieved in 2005/6 with the club finishing runners-up on goal difference. Additionally, the final of the Senior Cup was reached for the first time since 1979 but Horsham lost in extra time to Lewes. The club's first ever season in the Premier Division, in 2006/07, saw a creditable 8th place finish.