Football Club Levadia II Tallinn, known simply as Levadia II, was first established in 2000 under the name FC Levadia Tallinn. The club operated independently from its birth up until 2004, at which point it became the reserve team of FC Levadia Maardu, one of Estonia's most successful teams. FC Levadia Maardu have since relocated to Tallinn and have adopted the FC Levadia Tallinn name. Prior to the decision to function exclusively as a reserve team, Levadia II had enjoyed some significant success within Estonian football.
During their time as an independent football club, Levadia II experienced their greatest success in 2002, as they reached the final of the Estonian Cup. Here, they met their future parent club, Levadia Maardu, and defeated them 2-0 in order to lift the trophy; their first and, to date, only major honour. As a result, they gained entry to the preliminary round of the following year's UEFA Cup, marking their European debut. They were eventually eliminated from the competition by Israeli side, Maccabi Tel Aviv FC.
Since their decision to become a reserve team, Levadia II have played exclusively in Estonian football's second tier, the Esiliiga, and the team are ineligible to gain promotion to the country's top tier, the Meistriliiga. They have, however, enjoyed huge success in the division, winning four Esiliiga titles, with those successes coming in consecutive years in 2006, 2007, 2008 and 2009.
Estonian international, Aleksandr Dmitrijev, competed for the side during their time as an independent club, and later returned to their squad in 2005, whilst they were operating as Levadia II. Igor Morozov, another Estonia international, graduated from the Levadia II team and made his debut for the first team in 2006.
Levadia II's home matches are played at Maarjamäe Kunstmuruväljak in Tallinn, which is able to hold a capacity crowd of 1,500.