Tammeka was founded in 1989, as a youth academy. The club first began playing in the Estonian football league system in 2000, when Tammeka joined the III liiga. Tammeka's debut was a success, as the team ended the season with first place and 46 points out of the possible 60. Vitali Gussev was the team's top goalscorer with 22 goals. Tammeka was promoted to the II liiga and in 2001, to the Esiliiga. The club established itself in the Esiliiga by placing 6th in 2002 and 7th in 2003. Since 2003, Tammeka has also competed in the Estonian Cup. Tammeka triumphed in the 2004 Esiliiga season by winning the league and being promoted to the Meistriliiga, while Oliver Konsa was the league's top goalscorer with 25 goals.
In an effort to join the Tallinn and Narva based teams in the title fight, Tammeka merged with Maag and became Maag Tammeka. Despite pooled resources, the club lost several key players. Maag Tammeka finished the 2007 Meistriliiga season in 5th place and the 2008 season, in 7th. The club had more success in the Estonian Cup, as Maag Tammeka reached the 2007–08 Estonian Cup finals but was defeated by Flora 1–3. After the 2008 season, the sponsorship deal with Maag ended and Tammeka continued as an independent club once again.
Due to ended sponsorship deal, Tammeka had to operate with a smaller budget and lost several players. Reserve team coach Norbert Hurt was hired as manager and several reserve team players were promoted to the first-team squad. Despite a poor start in 2009, Tammeka managed to finish the season in 7th place. In 2010, the former Estonia national football team player Marko Kristal was hired as manager. Kristal started building the team around youth system players Albert Prosa, Kaarel Kiidron and Siim Tenno. Tammeka finished the 2010 Meistriliiga season in 6th place. Despite a good start in 2011, results began to drop in the second half of the season and Kristal was replaced as manager by the former Tammeka player Kristjan Tiirik. The team finished the season in 7th place, while Prosa scored 22 goals.
The performance Tammeka youth players didn't go unnoticed and Tammeka lost several key players in winter 2011–12, including Prosa, Kiidron and Tenno. This reflected on the team on 20 July 2012, Joti Stamatopoulos was brought in to replace Tiirik. Stamatopoulos failed to make a difference and Tammeka finished the 2012 Meistriliiga season in 10th place, amassing only 20 points. Despite finishing last, Tammeka wasn't relegated to Esiliiga, as Viljandi disbanded. In January 2013, Uwe Erkenbrecher was hired as manager. Despite growing financial troubles, Tammeka finished the 2013 season in 9th place and beat Tarvas 6–2 on aggregate in the relegation play-offs, securing their Meistriliiga spot.
In February 2014, Tammeka lost its Meistriliiga license due to failing to pay players' wages and refusing the reorganization plan proposed by the Estonian Football Association. The license to compete under the name Tammeka was granted to Jalgpallikool Tammeka (Football School Tammeka). Former Tammeka player Indrek Koser was hired as manager and the team finished the 2014 Meistriliiga season in 7th place. Tammeka finished the 2015 season in 9th place but avoided being relegated by defeating Tallinna Kalev 4–2 on aggregate in the relegation play-offs.