The club was founded in 2019 by three fans, following the dissolution of Varese Calcio, and have won the Terza Categoria in their debut season.

In 2020 Città di Varese merged with Busto 81, and gained the right to play in the 2020–21 Serie D Group A.

[6][7] As a matter of fact, Città di Varese adopted the historic colours of the football club founded in 1910 (red and white), but never openly claimed any inheritance of the ceased team.

[9][10] On 16 July 2020,[11] prior to the 2020–21 season, the club merged with Busto 81 (a club based in Busto Arsizio, no longer interested in pursuing the football activity) and obtained the right to participate in the Serie D Group A, Italy's fourth division.

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