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The club was established in 1904 as Pilton Yeo Vale, and were founder members of the North Devon League in the same year. They played in the league's first match, hosting Ilfracombe on 1 October; the visitors won 4–2 with several hundred in attendance. However, that was to be the only defeat all season in the league and club went on to win the inaugural league title. At the end of the season they adopted their current name.

After winning a second North Devon league title in 1908–09, they club switched to the Exeter & District League, where they remained until World War I. After the war they returned to the North Devon League, before rejoining the Exeter & District League. They won the league title in 1946–47 and were runners-up the following season, before joining Division Two of the Western League in 1948.

In 1949–50 Barnstaple won Division Two, earning promotion to Division One. In 1951–52 they reached the first round of the FA Cup for the first time, losing 5–2 to Folkestone in a replay. The club were league champions in 1952–53, and reached the first round of the FA Cup again in 1954–55, losing 4–1 at home to Bournemouth & Boscombe Athletic in front of a record crowd of 6,200. They reached the first round of the FA Cup for a third time in 1959–60, losing 4–0 at Exeter City.

The league was reduced to a single division in 1960, and the club reached the FA Cup first round again in 1972–73, before losing 2–0 at home to Bilston. The league expanded back to two divisions in 1976, with Barnstaple placed in the Premier Division. In 1979–80 they won their second Western League title, and finished as runners-up in the following two seasons. After finishing second-from bottom in 1990–91, Barnstaple were relegated to Division One. Three seasons later they won Division One, earning promotion back to the Premier Division.

They remained in the Premier Division until being relegated again at the end of the 2012–13 season, which saw them finish bottom of the Premier Division. However, they made an immediate return to the top division after winning Division One in 2014–15. The following season saw the club finish as runners-up in the Premier Division, earning promotion to Division One South & West of the Southern League. In 2021–22 they finished bottom of Division One South, resulting in relegation back to the Premier Division of the Western League.