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The club was established in 1884 and played their first match against Lynn Alexandria, winning 2–1. In 1899–1900 they won the Norfolk Junior Cup, a feat repeated in 1905–06. In the early 1900s the club joined the Norwich & District League. After World War I they did not rejoin the league until 1921–22. In 1935 they moved up to the Norfolk & Suffolk League. When the league merged with the East Anglian League to form the Anglian Combination in 1964, Fakenham were placed in the top division for the 1964–65 season, but were relegated at the end of the 1965–66 season. In 1970–71 they won the Norfolk Senior Cup for the first time. The following season they won Division One and returned to the Premier Division. They went on to win the Norfolk Senior Cup again in 1972–73 and 1973–74, as well as the Anglian Combination Senior Cup in 1978–79.

In 1988 Fakenham became founder members of Division One of the Eastern Counties League. After finishing second in 1991–92, a season in which they defeated Diss Town after a replay to win the Senior Cup again, the club were promoted to the Premier Division. In 1994 they won the Senior Cup again with a 4–0 win against King's Lynn in the final. They retained it the following season, beating Gorleston 2–1 in the final, before going on to win it for a seventh time in 1999. After finishing as runners-up in 1998–99, the club went into decline, and was relegated back to Division One in 2003–04, finishing bottom of the table. In 2005–06 they won the Division One Knock-Out Cup, but a slump in league form saw them finish bottom of Division One in 2008–09 and 2009–10.

Fakenham were Division One runners-up in 2013–14 season, earning promotion back to the Premier Division. In 2017–18 they finished third-from-bottom of the Premier Division and were relegated to Division One North. In 2021 the club were promoted to the Premier Division based on their results in the abandoned 2019–20 and 2020–21 seasons.