The club was founded in 1990 by local high school graduates as Nagano Elza S.C. Its orange and dark blue colors were selected to represent Nagano Prefecture. In 2007, the name was changed to A.C. Nagano Parceiro due to copyright issues, though the colors and the club's symbol (a lioness named Elza) remained intact.
The biggest rival of the club is neighboring Matsumoto Yamaga; the matches between them are called the "Shinshū derby". In their first season in the JFL, they achieved second place, but as J. League Associate Membership status was not granted due to technical problems (their stadium not having adequate capacity for professional football).