The history of the club dates back to 1990 when a group of local high school graduates started a football club Nagano Elza S.C. The team colors, orange and dark blue, represent Nagano Prefecture, and the team logo uses a lioness named Elza. In 2007, the club changed the name to A.C. Nagano Parceiro because the name "Elza" had already been trademarked. However, the club decided to keep the team colors and logo.
In 2011, the team's first season in the JFL, they finished in the second place, but the team was not qualified to for J. League Division 2. J. League Associate Membership status was not granted because the capacity of their stadium did not satisfy the league's requirement (minimum 10,000 seats).
In 2014, the team became the member of the newly founded J3 league, and later acquired the J. League Associate Membership in September as their stadium capacity met the required minimum number of seats.