The club was formed in 1901 and joined the Crewe and District League, and were crowned champions in their first three seasons from 1901-02 to 1903-04. In 1904-05 they finished in fifth place. They then joined the North Staffordshire and District League in the 1905-06 season finishing in third place. Up until the outbreak of World War I their highest league placing came in 1914-15 when they were runners-up. When the league resumed after the war Congleton spent one last season in the league, 1919-20 finishing as league champions.
In 1920 they joined the Cheshire County League, finishing as runners-up to Winsford in their first season, 1920-21. In 1939-40, the Cheshire League disbanded due to the War and so the club spent one season in the Macclesfield and District League, finishing in equal first place and winning the end of season play-off against Bollington Cross to be crowned champions.
When football resumed after World War II Congleton Town were once again back in the Cheshire County League. However, the struggled at first including finishing in last place in 1947-48. The club continued to struggle and spent the 1950s finishing toward the bottom of the table each season.
They began the 1960s still struggling culminating in a last place finish in 1964-65, before joining the Manchester League in the 1965-66 season, finishing in fifth place. Their stay in the league though lasted just three seasons and in the 1968-69 season they joined the Mid-Cheshire League, finishing in eighth place. In 1969-70 they were runners-up. They were runners-up again in 1971-72 then in 1973-74 they were crowned Mid-Cheshire league champions. The following season they finished third before winning the league for a second time in 1975-76. After another runners-up finish in 1976-77 they won the title for a third time in 1977-78, their last season in the league. In 1978 the club re-joined the Cheshire County League, ion the newly formed Second Division, finishing in seventh place in their first season back in the league, 1978-79. They won the league in its final season, 1981-82 before the league merged with the Lancashire Combination to form the North West Counties Football League in which they were founder members in 1982-83. In 1985-86 they were runners-up in the league, only missing out on the title on goal difference. In 1987-88 they joined the Northern Premier League in the newly created Division One, finishing in ninth place. In the 1989-90 season, they reached the First Round of the FA Cup after beating Witton Albion in the fourth qualifying round. In the first round they were drawn away to Football League club Crewe Alexandra where they lost 2-0. However, they struggled most years at the higher level of the Northern Premier League and after finishing in last place in the 2000-01 season, they were relegated to the North West Counties Football League Division One. They did though reach the fourth round of the FA Trophy where they lost 6-2 to Worksop Town. The club remained in Division One which was renamed the Premier Division for the 2008-09 season.
At the end of the 2008-09 season, Congleton finished fourth in the Premier Division, behind AFC Fylde, New Mills and Newcastle Town, with only the first placed side gaining promotion to the Northern Premier League. In 2009-10 the club again finished fifth after an excellent start to the season, a poor mid-season run of form cost them dearly.
Congleton Town Supporters Trust was formed in 2001. The trust aims to help the club through sponsorship and community projects.