Cowdenbeath F.C. traditionally date their origin to the merger of two local clubs, Cowdenbeath Rangers (formed 1880) and Cowdenbeath Thistle, which occurred in 1881. However, research by the club's historian suggests the Cowdenbeath Rangers name continued to be used at this time and the founding of Cowdenbeath F.C. should properly be dated to 1882, when another merger saw Rangers combine with a local club called Raith Rovers (formed 1881 and unrelated to the present Kirkcaldy club). The establishment of one club to represent the town thus coincided with the establishment of the Fifeshire Football Association that year. Cowdenbeath, who are the oldest surviving football club in Fife, lost in the inaugural Fife Cup final in 1883 but won the Cup for the first time in 1885.
The club's local success led to them being elected to join the Scottish League in 1905. They went on to record two consecutive Division Two championships in 1914 and 1915, but under the election system which then applied, they weren't chosen for promotion to the top flight. Promotion was finally achieved for the first time in 1923-24, and was immediately followed by a fifth place finish in Division One. Cowden spent a decade in the top division at this time, and had three players capped by Scotland.
The club was relegated in 1934 but claimed their third Division Two championship in 1938-39. This feat was in no small part aided by Rab Walls' 54 League goals - the second highest seasonal total in Scottish League history. However, the outbreak of the Second World War cut short Cowden's return to Division One, and the club closed down for the duration of hostilities. When peacetime football resumed, the club were controversially placed in the new (second tier) B Division.
While a 1949 League Cup success over Rangers at Ibrox was a highlight of the early post-war period, Cowden struggled to return to the elite level of Scottish football. This was finally achieved under popular manager Andy Matthew in 1969-70, but the solitary season in Division One that followed remains the club's only top flight campaign since the 1930s. More recently, hopes for the future were raised when Cowden were promoted to the First Division in 1992, but they soon slumped back to the basement of the Scottish League amidst a run of 38 League games without a win at Central Park.
A more professional approach was ushered in with the appointment of former Scotland defender Craig Levein, who had begun his playing career with Cowdenbeath, as manager in 1997. Promotion from the Third Division was achieved in 2001, although they would be relegated again two years later. After a third place finish in 2004-05, the 2005-06 campaign saw the team achieve their first divisional title win for 67 years with player-manager Mixu Paatelainen.