Harju JK was founded in August 2009 with the goal to promote local and youth football, as well as to develop local players for Estonian youth national teams or for potential transfers abroad.

In 2015, they entered the Estonian football pyramid at the sixth tier and achieved promotion to the fifth tier already in their first season. In 2019, Harju JK appointed Portuguese Victor da Silva as head coach, who took them through four consecutive promotions to the second tier. During that time, Harju’s team consisted mostly of their youth system players. As a result of this, first transfers of Estonian youngsters abroad followed – Karel Mustmaa signed a three-year professional contract with Benfica U17 in 2021 and Imre Kartau moved to Venezia F.C U18 the following year.

Harju won their first Esiliiga in 2022 season and earned promoted to Premium Liiga for the first time in their history. They finished last in their debut system and got relegated right back to the second tier in 2023. There, Harju had an excellent season, only losing twice, and earned promotion back to the top in 2024.