The club was established as Newport Pagnell Wanderers in 1963, following a meeting between a group of players and Town Clerk Frank Hall. They joined the North Bucks & District League in 1964 and won the Division Three Shield in their first season. After winning Division Three in 1965–66 and Division Two in 1966–67, the club were promoted to Division One. They went on to win the Division One title in each of the next three seasons, with the reserve team winning Division Two in 1968–69 and 1969–70. In 1971 the club moved up to Division One of the South Midlands League, before being renamed Newport Pagnell Town in 1972.
Newport Pagnell were Division One runners-up in 1972–73, after which they transferred to Division Two of the United Counties League. The club finished second in Division Two in 1975–76, earning promotion to Division One. After winning the Division One title in 1981–82, they were promoted to the Premier Division. The club finished bottom of the Premier Division in 1985–86 and was relegated back to Division One. They were Division One runners-up in 1991–92, earning promotion back to the Premier Division, but were relegated to Division One after finishing bottom of the Premier Division in 1996–97.
In 2001–02 Newport Pagnell were Division One champions and were promoted to the Premier Division, as well as winning the Berks & Bucks Intermediate Cup. They were Premier Division runners-up the following season. The club won the Berks & Bucks Senior Trophy in 2009–10 and retained it in 2010–11. At the end of the 2018–19 season they were transferred to the Premier Division of the Spartan South Midlands League. Two seasons later they were transferred back to the United Counties League, joining the Premier Division South. In 2021–22 the club won the FA Vase, defeating Littlehampton Town 3–0 in the final at Wembley Stadium.