Tammeka was founded in 1989 as a youth football club and made its name in the 1990s with Tammeka Cup. In 2000, Tammeka's first homegrown started playing in the Estonian League system, rising quickly to the second-tier Esiliiga.
In 2004, Tammeka won Esiliiga in the last game of the season and was promoted to the highest division of Estonian football - the Meistriliiga. The first game of the freshly promoted Tammeka brought the club its biggest win in Meistriliiga to date, when the blue-and-whites destroyed Tallinna Dünamo 9:0. The young team was however quickly brought to ground and the club finished its first season in the top division with 7th place. The next season followed in the same rhythm.
In 2006 Tammeka merged with city rivals Tartu Merkuur (known as JK Maag Tartu for sponsorship reasons at the time) to form JK Maag Tammeka. This new symbiosis brought the club its highest league finish (5th in 2007) and a place in the 2007-2008 Estonian Cup final. However, the unified club failed to bring European football to the city in two seasons and in 2009, Maag was dropped from the club's name after the company withdrew its sponsorship.
Tammeka started the 2009 season with a brand new and young team, which had a hard time adapting to the demands of Meistriliiga. The struggling club changed ownership in the summer of 2009 and with the arrival of several foreign players secured its place in the league. In 2010 and 2011, the club again thrived under the management of Marko Kristal as the new "Golden Generation" of players - notably Albert Prosa, Kaarel Kiidron and Siim Tenno - matured and brought stability to the club.
Before the 2012 season, Tammeka was forced to sell several of its best players. The club struggled the whole season and finished last in the league but still retained its place in Meistriliiga after FC Viljandi disbanded.
In 2013, the club brought in an experienced German manager Uwe Erkenbrecher. Tammeka hit financial trouble on the second half of 2013 season, failing to pay players wages for four months but refused the reorganization plan proposed by Estonian Football Association. In February 2014 Tammeka were stripped of their Meistriliiga license. Tammeka entry was later granted for 2014 season to Jalgpallikool Tammeka (Football School Tammeka), a financially independent part of the club run by some of the former employees of football club Tammeka.