Jalgpalliklubi Tammeka II Tartu, often known by the more simply name of Tammeka II, was founded in 2006 under the name Maag Tammeka II. The team was created to serve as the reserve team for JK Tammeka Tartu; a team founded in 1989, who play in Estonia's top tier. Tammeka II adopted their current name ahead of the 2009-10 season. Over the years, the team have bounced between the country's second and third tiers, the Esiliiga and II Liiga, respectively.
Due to their status as a reserve team, Tammeka II are not eligible to gain promotion to the country's top tier. As a result, their sole chance of achieving major glory comes in the Estonian Cup. In the 2007-08 season, they reached the quarter final stage of the competition, before being eliminated by the eventual winners, FC Flora. To date, this remains their best performance in the tournament.
The team began competitive play in the Esiliiga in 2007 and finished the season in 5th place. The following year, Tammeka II's performances declined and they finished 7th. At the conclusion of the season, they were moved down to Estonia's third tier. In their first season in the division, they finished as league runners up. A 7th place finish followed in 2010, before the club were able to push on and finish as runners up once again in 2011. This time, as a result of their performances, Tammeka II gained promotion back to the Esiliiga. However, the 2012 season saw them finish in a disappointing 8th place and the side were only able to cling to their place in the division on a technicality.
Some of the most notable players to have played for the club include Georgi Ivanov and Hannes Tiru.
Tammeka II's home matches are played at Tartu Annelinna Kunstmuruväljak, which is able to seat 150 supporters and hold a maximum of 500 people, when standing room is included.