The club was founded in 1975.[1] In 2020, Vaipuna SC finished second in the regional Upolu Senior League. That season, Vaipuna player John Michael Tumua was the co-top scorer in the league.[2] Vaipuna SC finished the 2021 Samoa National League season in second position in the league table, one point behind champions Lupe o le Soaga SC. That season, John Michael Tumua was the league's top scorer with forty-five goals.[3] The club finished the 2022 season undefeated. However, they were again the league runners-up, being edged out by Vaivase-Tai FC on goal difference.[4]
Youth
Vaipuna SC also field youth sides.[5] In 2019, the club's under-12 team won the championship in its division.[6]