The club was established in 2000 following the amalgamation of the Warkauden Pallo-35 and Varkauden Työväen Palloilijoiden clubs. The new club has now played 10 consecutive seasons in the
Kakkonen (Second Division), the third tier of
Finnish football from 2001 to the present day. In 2002 the club finished in top position in the West Group but failed to progress in the Promotion Play-offs. The 2008 season has been the most successful to date for Warkaus JK with the club getting through to the quarter-finals of the Suomen Cup before going out 2–0 away to
Helsingin Jalkapalloklubi. In Group A of the
Kakkonen the team finished in second place, 5 points behind Klubi 04. In 2009, Warkaus JK won the final of Työväen Urheiluliiton Cup (Workers' Sports Federation Cup) for the first time in their history. ==Season to season==