The club was founded in 1907 by Cesare Lanza and Nicolò Pessano and disputed its first championship in the 1910. Savona's history includes two seasons in the Italian Football Championship in the 1920s, and many seasons in Serie B (the last one in 1966-67).
After spending some time in Serie C the team was relegated to Serie D and has remained there for about 20 years, only having two seasons in Serie C2 between 2002 and 2004 before being relegated back. In this period Savona has won its only trophy, the Coppa Italia Dilettanti in 1991.
In the season 2009-10 it was promoted from Serie D to Lega Pro Seconda Divisione but on 23 December 2011 the club, in strong financial difficulty, was declared in bankruptcy by the court of Savona. On 13 March 2012 Aldo Dellepiane, at the auction proceedings took over the company for one euro, taking on a proportionally portion of the debts, saving it from radiation. On its first season under the new company, Savona won promotion to Lega Pro Prima Divisione. In the 2013–14 season, Savona emerged as a surprise package for Serie B promotion, reaching sixth place in the final standings and eliminating Vicenza in the subsequent promotion playoffs, before being defeated by eventual winners Pro Vercelli in the semi-finals. In 2014-2015 season, Savona played in Lega Pro, struggling to avoid relegation in Serie D.
In summer 2015 it was penalized of 6 points for sporting fraud.