This article is about the club which was known as FC Levadia Tallinn between 2000–2004. For its current parent club, which was known as FC Levadia Maardu between 1998–2004, see FCI Levadia Tallinn.
Founded as Levadia Tallinn, it was the reserve team of Levadia Maardu from 2000–2004. In 2004, Levadia Maardu moved to Tallinn and became the new Levadia Tallinn, while the reserve team became Levadia II.
Reserve teams in Estonia play in the same league system as the senior team, rather than in a reserve team league. They must play at least one level below their main side, however, so Levadia U21 is ineligible for promotion to the Meistriliiga but can play in the Estonian Cup. As Levadia Tallinn, the club has won 1 Estonian Cup trophy.
In 2017, Tallinna FC Levadia and FCI Tallinn joined, which resulted in their reserves also joining and becoming Tallinna FCI Levadia U21
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