Vaprus was formed in May 1922, as Spordiselts Vaprus (''''). The club was active in various sports and credited for organising the first intercity running competitions from Pärnu to
Tallinn and from Pärnu to
Riga. However, the club failed to reach the heights of their rivals
Pärnu Tervis and in 1937, Vaprus merged with several other local sporting clubs to form Pärnu Kalev. The club was re-established in 1999 as an amateur team playing in the lower leagues. In 2003, several local clubs merged with Vaprus, including former top league club Pärnu Levadia, forming a working football club. Vaprus won the
2005 Esiliiga season and was, for the first time in the club's history, promoted to Estonia's top-flight football league
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. In 2010, Vaprus formed a united team
Pärnu Linnameeskond with
PJK and Pärnu Kalev. Vaprus itself continued to only operate in youth football until 2014, when they entered their senior team to Estonian lower leagues. Pärnu Linnameeskond reached Estonian top flight in
2015, but broke up after two seasons with Pärnu Vaprus inheriting their league spot for
2017. After an eight-year absence, Vaprus returned to top-flight football and moved to the newly renovated 1,501-seat
Pärnu Rannastaadion. The club finished the season in last place, but managed to avoid relegation due to
Sillamäe Kalev's bankruptcy. However, the club again placed last and was relegated in the following
2018 season. Vaprus lifted the second division title in
2020 and returned to Meistriliiga, where they finished bottom of the table in both
2021 and
2022, but avoided relegation on each occasion due to
Viljandi Tulevik and
TJK Legion withdrawing from the top flight for financial reasons. Pärnu Vaprus appointed
Igor Prins as their manager for the following
2023 season and recorded their most successful season in the club's history, surprisingly occupying 3rd place until matchday 27 and finishing the season in 6th place with 48 points, despite being considered as clear relegation candidates at the start of the year. Vaprus finished the following year in 7th place, before repeating their highest 6th place finish in
2025, accumulating a club record 49 points. During the season, the club's 16-year-old forward
Marten-Chris Paalberg was called up to the Estonian national team. == Kit manufacturers and shirt sponsors ==