The first team from Crotone, Milone Crotone, was founded in 1910 and participated in several minor leagues including Prima Divisione (which later would be known as Serie C). Following World War II, a new club, Unione Sportiva Crotone replaced the previous one, playing seven seasons in Serie C.
In 1963 the club was relegated to Serie D, but returned to the third division the following year, remaining there for fourteen consecutive seasons, missing promotion in 1977 when finishing third behind Bari and Paganese. In 1978, following the Italian football league reorganisation, Crotone was relegated to Serie C2 and the following year was declared bankrupt. A new club, Associazione Sportiva Crotone, began competing again in the Prima Categoria (eighth division).
Crotone was promoted to Serie C2 in 1984–85, but only for one season. The team's name was changed to Kroton Calcio, and the club was promoted again to C2 after the 1986–87 season, where it played until 1991. A second bankruptcy led to the foundation of Football Club Crotone Calcio with Raffaele Vrenna as chairman, starting in the Promozione (7th level). Crotone gained successive promotions to Serie C2 and C1, winning in the play-offs against Locri and Benevento, respectively.
Under Antonello Cuccureddu, Crotone first reached Serie B in 2000, returning to the second level two seasons later. Again in division two in 2004, after disposing of Viterbese in the promotion play-offs, it remained in the category until the 2006–07 season.
After being beaten by Taranto in the 2008 play-offs, Crotone returned to the second division the following season, defeating Benevento.
The team was promoted to the Italian top flight (Serie A), for the 2016–17 season for the first time in its history. They finished in 17th, securing a place in the next Serie A season, by beating Lazio 3–1 on the last matchday, knocking down Empoli as they lost their match against Palermo.
The following season Crotone failed to avoid relegation after their loss against Napoli in the last match of the Serie A campaign, returning in Serie B after two seasons.