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Korvpalliklubi Pärnu (English: Basketball Club Pärnu) was founded in 2000. In 2006, the team joined the Korvpalli Meistriliiga (KML), the top tier of Estonian basketball. They also made their debut in the Baltic Basketball League (BBL) in 2012. On 12 July 2017, KK Pärnu announced that they will withdraw from the forthcoming KML season due to financial difficulties. However, the team would stay in the KML after reaching an agreement with KK Paulus.

In 2018, the Estonian-Latvian Basketball League was formed. Pärnu Sadam reached the playoffs in the league's inaugural season, where they lost to BK Ventspils in the quarterfinals. In the 2019 KML Playoffs, Pärnu Sadam defeated AVIS UTILITAS Rapla in the quarterfinals, but lost to BC Kalev/Cramo in the semifinals. In the third-place games, they defeated TalTech. Pärnu Sadam made the KML Finals for the first time in team history in 2021. However, they could not overcome BC Kalev/Cramo and lost the series three games to one. The team finished the 2021–22 Estonian-Latvian Basketball League season in third place. They lost 81–83 to KK Viimsi/Sportland in the semifinal but beat BK Ogre 84–77 in the third place game. In the 2022 KML Playoffs, Pärnu Sadam defeated AVIS UTILITAS Rapla the quarterfinals and the defending champion BC Kalev/Cramo in the semifinals to advance to the finals for the second consecutive year. They swept Tartu Ülikool Maks & Moorits in three games to win their first Estonian championship. Andris Misters was named the KML Finals MVP.

Heiko Rannula, who had coached the team since 2014, left Pärnu after the 2021–22 season to join BC Kalev/Cramo. After failing to qualify for the Champions League, the team played in the FIBA Europe Cup, but didn't advance past the regular season. Pärnu Sadam were unable to defend their KML title, falling in the semifinals to Tartu Ülikool Maks & Moorits. They did, however, beat Viimsi/Sportland in the third-place series.