In 1956–57 Clacton won the East Anglian Cup and reached the fourth and final qualifying round of the FA Cup, but lost 3–2 at home to Yiewsley. After finishing fifth in 1957–58 the club moved up to the South-East Division of the Southern League. Although they finished second from bottom in their first season, the following year they won the newly renamed Division One, and were promoted to the Premier Division. In their first season in the Premier Division they reached the first round of the FA Cup for the first, and to date only time, but lost 3–1 at home to Southend United. However, after finishing twenty-first out of 22 clubs in 1962–63, they were relegated back to Division One, and after a mid-table finish in 1963–64, returned to the Eastern Counties League.