FCI Levadia Tallinn was founded in 1998 in Maardu, with its origins linked to FK Olümp Maardu. After the club was taken over by the Levadia company, the team was renamed Maardu FC Levadia. In autumn 1998, the club won promotion to the top division, and within a year it had already achieved the most important success of its young history. In 1999, Levadia won the Estonian championship and the Estonian Cup. The following year, the club retained its league title, finishing both of its first two seasons in the top flight unbeaten.
Levadia's early history was centred on Maardu, but the club soon moved its sporting base to Tallinn. In 2004, the first team was formally established in the capital, beginning a long period at the top of Estonian football. Viktor Levada became one of the key figures in the organisation's history, with his name forming part of the club's identity. In 2017, Levadia merged with FCI Tallinn, previously known as FC Infonet. From 2018, the first team has competed under the name FCI Levadia.
Domestic competition has been the foundation of Levadia's success. The club has won numerous Estonian championships and Estonian Cups, becoming one of the two leading forces in Estonian football since the restoration of independence. The beginning of the 21st century was particularly successful, with Levadia regularly collecting major domestic trophies. In 2004, under coach Tarmo Rüütli, the club won both the Estonian championship and the Estonian Cup. In 2009, Levadia claimed its seventh league title and its fourth consecutive championship.
European qualifying rounds have also played an important role in the club's history. In 2007, Levadia came close to eliminating Red Star Belgrade. After losing 1–0 in Serbia, the Estonian side won the return leg 2–1 but were eliminated under the away-goals rule, which was still in force at the time. One of Levadia's goals was scored by Konstantin Nahk from long range. The tie remains one of the most memorable European encounters in the club's history.
Levadia produced an even bigger upset in the 2009 UEFA Champions League qualifying rounds by eliminating Wisła Kraków. The first leg in Kraków ended 1–1, while a late goal from Vladislav Ivanov gave Levadia victory in the return match in Tallinn. The Estonian champions were subsequently eliminated by Debreceni VSC, losing both matches 1–0. Earlier, in 2006, Levadia had also faced Newcastle United in the UEFA Cup, losing 1–0 at home and 2–1 away.
In 2024, FCI Levadia enjoyed one of the most successful seasons in its history. Under Curro Torres, the club won the Estonian championship, the Estonian Cup and the Estonian Super Cup, completing a domestic treble. In 2025, Levadia finished second in the league behind Flora Tallinn.
FCI Levadia plays its home matches at A. Le Coq Arena in Tallinn, Estonia's principal football stadium. The club has retained its distinctive green-and-white colours, which have become an important part of its identity. Levadia is one of the most successful Estonian clubs of the post-independence era, combining a substantial domestic trophy record with a long history of participation in European qualifying rounds.