The club was established in November 1871, making it the oldest club recognised by the Oxfordshire County Football Association. They joined the ReadingTemperance League and were league champions in 1912–13, finishing as runners-up the following season. In 1931 the club joined Division Two West of the Spartan League. After two mid-table finishes, the club won the division in 1933–34, earning promotion to Division One. In 1936–37 they were Division One champions and were promoted to the Premier Division. However, they finished bottom of the Premier Division the following season, winning only one match, and were relegated back to Division One. When the Spartan League was suspended in 1939 due to World War II, Henley spent the 1939–40 season in the Great Western Combination. When football resumed after the war, Henley returned to the Spartan League and were placed in the Western Division. They finished second-from-bottom and missed out on a place in the Premier Division the following season. In 1952 they rejoined the Great Western Combination, becoming members of Division One. Despite finishing bottom of the division in their first season in the league, they were not relegated to Division Two. However, after finishing bottom of the division again in 1954–55 the club left the league. In 1957 Henley joined Division One of the Hellenic League. They were Division One champions in 1963–64, resulting in promotion to the Premier Division. However, the following season saw them finish in the bottom two in the Premier Division, resulting in relegation back to Division One. They won Division One again in 1967–68 without losing a match, earning promotion to the Premier Division. After losing their Reading Ground in 1971 the club dropped out of the Hellenic League. Later regrouping in the Wycombe & District League, the club were promoted to the Senior Division at the first attempt and won both the league and the Wycombe Senior Cup in 1978–79. Henley were founder members of the Chiltonian League in 1984. When it gained a second division the following season, they were placed in Division Two. The division was renamed Division One in 1987 and the club went on to win the division in the 1987–88 season, earning promotion to the Premier Division. They were relegated back to Division One at the end of the 1990–91 season, but a fourth-place finish in Division One in 1992–92 was enough to secure promotion back to the Premier Division. The club won the Premier Division title in 1999–2000. At the end of the season the Chiltonian League merged into the Hellenic League, with Henley becoming members of Division One East. They won the division at the first attempt, earning promotion to the Premier Division. After finishing bottom of the Premier Division in 2005–06, Henley were relegated to Division One East. They remained in the division until the end of the 2010–11 season, when they were promoted back to the Premier Division as Division One East runners-up. However, they only spent one season in the Premier Division before being relegated back to Division One East due to their ground failing to meet the necessary criteria. In 2015–16 the club finished third in Division One East and were promoted to the Premier Division; the season also saw them win the Reading Senior Cup with a 5–3 defeat of Binfield at the Madejski Stadium. However, they finished bottom of the Premier Division the following season and were relegated back to Division One East. In December 2017 the club resigned from the Hellenic League. The 2018–19 season saw the club restart in Division Three of the Thames Valley Premier League, which they went on to win as champions, earning promotion to Division Two.
Ground
The club played at Reading Road from 1901 until 1971. They then played at temporary grounds during the 1973–74 season before moving to the Triangle Ground on Mill Lane.