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The club was established by Tommy Watson in 1998 as the Lincolnshire Soccer School, with Watson playing for and managing the club. As LSS Lucarly's, they joined the Lincolnshire League in 2003, where they played for two seasons. In 2005 the club transferred to the Premier Division of the Central Midlands League in 2005. However, after one season they left to join Division One of the Humber Premier League. After finishing third in their first season in the division, they were promoted to the Premier Division. In 2008 the club adopted their current name.

Cleethorpes pulled out of the Humber Premier League during the 2009–10 season, but rejoined the Lincolnshire League for the 2010–11 season, which saw them win the Supplementary Cup. After winning the league and Challenge Cup in 2011–12, they were promoted to Division One of the Northern Counties East League. In 2013–14 they won Division One, earning promotion to the Premier Division. In 2015–16 they won the League Cup, beating Tadcaster Albion 3–2 in the final. The following season saw the club win the Premier Division, earning promotion to Division One South of the Northern Premier League. They also won the Lincolnshire County Senior Trophy with a 1–0 win over Deeping Rangers in the final, as well as reaching the final of the FA Vase at Wembley, where they lost 4–0 to South Shields.

In 2018–19 Cleethorpes won the Lincolnshire Senior Cup for the first time, defeating Stamford 5–3 on penalties after a 3–3 draw.