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The club was established in 2010 after King's Lynn F.C. were wound up in 2009. They were admitted to the Premier Division of the United Counties League and were runners-up in their first season in the league, also reaching the semi-finals of the FA Vase, where they lost 6–2 on aggregate to Coalville Town. After finishing as runners-up again in 2011–12 the club were promoted to Division One South of the Northern Premier League. They won Division One South at the first attempt, earning promotion to the Premier Division. In 2015 the club were transferred to the Premier Division of the Southern League. In 2016–17 they won the Norfolk Senior Cup, beating Fakenham Town 2–0 in the final. The club were runners-up in the Southern League Premier Division in 2017–18, qualifying for the promotion play-offs. After beating Weymouth 3–0 in the semi-finals, they lost 2–1 to Slough Town in the final. The club were placed in the Premier Division Central for the 2018–19 season, going on to finish as runners-up and qualifying for the play-offs. After defeating Stratford Town and Alvechurch, they were promoted to the National League North following a 3–2 win against Warrington Town in the super play-off final.

The 2019–20 season was abandoned due to the coronavirus pandemic with the club second in the league, two points behind leaders York City with two games in hand. The National League later decided the final league table would be based on points-per-game, resulting in King's Lynn being declared champions, earning promotion to the National League. In 2020–21 the club reached the first round of the FA Cup for the first time after Notts County were forced to cede their fourth qualifying round tie due to a COVID outbreak in their squad; King's Lynn went on to defeat League Two club Port Vale 1–0 at Vale Park in the first round, before losing 6–1 at Portsmouth in the second.

Another FA Cup first round appearance in 2021–22 ended in a 1–0 home defeat by Walsall, while the league season ended with King's Lynn being relegated from the National League back to the National League North. In 2022–23 they reached the FA Cup first round again, winning 1–0 at Doncaster Rovers to progress to the second round where they lost 3–0 to Stevenage. They went on to finish as runners-up in the National League North, but lost 4–1 to Kidderminster Harriers in the play-off semi-finals.

In January 2024, the club announced a strategic investment and partnership deal with the Singapore-based Turn Sports Investment.