Pärnu Linnameeskond was founded in 1922, following the merger of Vaprus, Pärnu and Pärnu Kalev. 2011 Esiliiga season was the team's first season under the new name. The club has played in the Meistriliiga since 2015.
FC Pärnu Levadia was established in 2000. The team was formed out of young local players from Tervis Pärnu and was sponsored by Viktor Levada, who was looking to restructure Levadia's farm club system. 2000 and 2001 saw Pärnu Levadia winning two successive promotions, first to Esiliiga and then to Estonian top-flight Mesitriliiga, where the team was strengthened by some players from the Levadia system, who were not getting enough playing time at either Levadia Maardu (now Levadia Tallinn) or Levadia Tallinn (now Levadia's reserve team). Pärnu Levadia finished bottom of the Meistriliiga in their first and only season in the top-flight. Following the unsuccessful 2002 season, Viktor Levada decided to withdraw his sponsorship from Pärnu and Pärnu Levadia's Esiliiga slot was taken over by Vaprus Pärnu. Pärnu Levadia players who had no contract affiliation with Levadia also joined Vaprus for the following Esiliiga season.
Vaprus was formed in May 1922, as Sporting Society Vaprus. Founding members included Johann Tamm (Vaprus president 1922–1927), Johan Põntson (ten-time Estonian wrestling champion), weightlifter Arnold Luhaäär (1928 Summer Olympics Silver and 1936 Summer Olympics Bronze) and William Puust (Pärnu Football Club founder). Vaprus competed in the local Pärnu football championships, winning in 1927 and 1934. In 1937 the club merged with several other sporting clubs to form Pärnu Kalev.
The club was re-established in 1999 and competed in the III liiga. Vaprus won the Western Conference in 2000 and earned promotion to II liiga. Following the 2002 Estonian football season, Vaprus took over Pärnu Levadia's Esiliiga slot. The originally re-established Vaprus continued as the club's reserve team, while the first team was predominantly made of former Pärnu Levadia players. The same season, Vaprus suffered relegation from the Esiliiga after the club's license was revoked by the Estonian Football Association halfway through the season. Vaprus won the 2005 Esiliiga season and was promoted to Meistriliiga. The club finished their first Meistriliiga season in 7th place. Vaprus finished the 2008 Meistriliiga season in 10th place, but managed to avoid direct relegation due to disbandment of TVMK. However, the club was still relegated after losing the relegation play-offs against Paide Linnameeskond.