Founded in 2009, the club competes in the Meistriliiga, the top flight of Estonian football, following promotion from the 2024 Esiliiga as league champions.

[3] Harju JK won Esiliiga in the 2022 season and were promoted to Estonian top flight Premium Liiga for the first time in its history.

Despite a number of strong performances,[4][5] the club finished the 2023 season in last place with 23 points and were relegated back to Esiliiga.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.