Viimsi JK was founded in 2016, when HÜJK Emmaste, a club founded in 2000 that represented the
Hiiumaa island, and Viimsi MRJK, a club which focused on youth football and was founded in 2007 by
Martin Reim, merged. The new club inherited Emmaste's league spot and most senior players, while youth players, management and the stadium were provided by MRJK. In 2021, Viimsi JK finished first in
Esiliiga B and gained promotion to
Esiliiga, the second-highest division in Estonian football. After finishing in second place in the
2023 season, the club faced
Tartu Tammeka in the top flight promotion play-offs, but lost 1–6 on aggregate. Viimsi reached the
2023–24 Estonian Cup semi-finals, where they lost to the eventual winners
FCI Levadia 0–1 after extra time. Viimsi finished the
2024 league season again in second place and faced
Tallinna Kalev in the promotion play-offs, narrowly losing 1–2 on aggregate after extra time. For the third consecutive season, Viimsi finished the season as runners-up, this time losing the promotion play-offs to
Kuressaare. == Stadium ==