The current Alton FC was formed by the merger of Alton Town FC and Alton United Youth FC in 2016.
Previously the senior section (Alton Town FC) was formed in 1990 when Alton's two senior clubs, Alton Town and Bass Alton, amalgamated. Alton Town had been fantastically successful, winning everything in Hampshire in the period from 1948 to 1956 including Hampshire leagues Divisions 3, 2 & 1 (1948, 1949 & 1958), the Hampshire Intermediate Cup in 1949, the Russell Cotes Cup in 1949 and the Hampshire Senior Cup in 1958.
Alton Town first joined the Hampshire League in 1947 and won Division 3 East in their first season. More success followed with the Division 2 title in 1948/49 and they also won the Russell Cotes Cup and Hampshire Intermediate Cup that year. Although they dropped to Division 2 for one season in 1954/55, they bounced back immediately and went on to win both the Division 1 championship and the Hampshire Senior Cup in 1957/58. They stayed in Division 1 until they left in 1973 to join the Athenian League Division 2 which they won in their first year. After an initial period of success in that league the Club found itself unable to compete and dropped down to the Combined Counties League before returning to the Hampshire League in 1984, starting at the bottom in Division 3. They found themselves in Division 2 in 1986/87 by dint if winning the Division 2 title for the third time.
Bass Alton started life as Courage & Company (Alton) FC and joined the Hampshire League in 1928/29. The following year they were in Division 2 and then won promotion to Division 1 where they stayed until being relegated to Division 2 in 1938/39, just before the club was disbanded for the War.
Courage rejoined the North Hants division briefly in 1954/55 before beginning their longest spell in the County League in 1972/73 when they entered Division 4. Promoted to Division 3 in 1975, they only lasted two years before dropping to Division 4 again. In 1979/80 the Club changed its name to Bass Alton FC and its fortunes changed with the name as they won promotion in successive years to Division 3 in 1979/80, to Division 2 in 1980/81 and to Division 1 as Division 2 runners-up and the end of the 1982/83 season after a 45-year absence.
Since the amalgamation, the Club has played in the Hampshire League and achieved promotion to the Wessex League by topping the Premier Division in 2002, moving to the Premier Division of the Cherry Red Records Combined Counties League from season 2013-14 and moved back to the Wessex League from season 2015-16.