Workington A.F.C originally were one of the founder members of the Cumberland Association League in 1888 and played at Lonsdale Park. In 1894 they moved to the Cumberland Senior League, then in 1901 joined the Lancashire League.T he league closed two seasons later, and they returned to the Cumberland Senior League. In 1904 the club were admitted to the Lancashire Combination. In the 1910 season they decided to economise and join the North Eastern League. But, after only one season, the club folded.

The new Workington A.F.C. was born in 1921 and immediately joined the North Eastern League. During the 1933/34 season, the club managed its best-ever FA Cup performance, reaching the 4th round, before losing to Preston North End. Later in the decade, the club moved to its present home, Borough Park. In 1951 the club was voted into the Third Division North of The Football League replacing New Brighton.

Their first season in the League was a sign of things to come; the club finishing rock bottom, and only improving by one place the following year.

From 6 January 1954 to 15 November 1955 the club was managed by Bill Shankly, who would achieve fame between 1959 and 1974 with his success at home and abroad as manager of Liverpool.

During the 1957/58 season they played the great Manchester United team known as the Busby Babes at home in the 3rd round of the FA Cup, attracting a record crowd of 21,000. This was just a month before eight of the United players lost their lives in the Munich air disaster.

However, at the end of that season, the club dropped into the new Fourth Division under a reorganisation of the Football League which saw the abolition of the regionalised Third Divisions.

In 1964, player-manager Ken Furphy (pictured) led them to 3rd position, earning promotion to the Third Division. During both the 1963/64 and 1964/65 season, they made it to the quarter-finals of the League Cup, where they lost to West Ham United and Chelsea (in a replay) respectively. During the latter cup run, the club beat Lancashire neighbours Barrow 9–1, a record which remained until the mid-1980s.

In 1966 they finished in 5th place, narrowly missing out on promotion to the Second Division, but next year finished bottom, and were relegated back to the Fourth Division. In 1974 and 1975 the club finished 23rd out of 24 and in 1976 they finished bottom. In 1977 the club won only four games, and again finished bottom of the League with attendances falling well below the 1,000-mark. This poor run led to the club being voted out of the League in the summer of 1977, being replaced by Wimbledon.
The club dropped into the Northern Premier League , but failed to trouble the top teams, never finishing higher than 7th, before they were relegated to the NPL First Division in 1988. They continued to struggle, eventually being relegated to the North West Counties League in 1998. However, the club managed to win the League at their first attempt (also their first ever championship). After a 2–0 defeat at Kidsgrove Athletic on 27 February 1999, manager Peter Hampton set the squad a challenge, win their last 14 games and they would win the league. Sure enough after winning the next 13 games Workington squared up to league leaders Mossley at Borough Park in front of a 2,281 spectators, a league record only beaten by the formation of F.C. United of Manchester. Workington ran out 2–1 winners with goals from Stuart Williamson and substitute Grant Holt. Workington became the first club to return to the NPL First Division at the first attempt.

As a result of a 7th place finish in 2004, the club moved up to the NPL's Premier Division during the non-league restructuring. They then continued their upward movement by winning the first-ever NPL promotion play-offs (after finishing in 2nd place) to win promotion to the Conference North.

Following a mid-table finish in their first season in Conference North, the 2006–07 season saw Workington finish in third place and qualify for the promotion play-offs where they lost 2–1 against Hinckley United. After two mid table finishes the following seasons, Workington made the play offs again in 2009/10 this time going down 4–1 on aggregate to Alfreton Town in the semi final.