The club was founded in 1919 and played at the top level of football between 1938 and 1947, before being disqualified from the league due to manipulation of results. The club then played in the top flight sporadically, just four more seasons before the establishment of a separate Czech league in 1993. The club went on to spend a three-year spell in the Czech First League before returning to the second division in 1996. After regaining promotion to the First Division in 2002, the team recorded a number of steady performances in the league, recording a 7th-place finish twice, in 2003 and 2004, and later finishing 8th in the 2007–08 season.
At the start of the 2008–09 season the team struggled, scoring just 9 points from their opening 16 matches. The club were battling relegation as the season came to a close despite a late run of good form in which they enjoyed an unbeaten run of six matches, including five wins. They needed a win in their last match of the season against Baumit Jablonec to avoid relegation, but conceded after just two minutes, trailing 5–1 at half-time and finally losing by a 6–1 scoreline, their biggest league defeat in 62 years, and dropped out of the Czech First League after seven years in the top flight. The club started the 2010–11 Czech 2. Liga with a sequence of four straight wins, and began the following season with a sequence of six matches undefeated before losing to MFK Karviná in 2011–12 Czech 2. Liga, although they did not manage to sustain their form on either occasion, finishing 11th and 10th respectively. The club marked the start of the 2012–13 Czech 2. Liga by changing their name, manager and captain, bringing in Aleš Křeček to manage the team, installing Tomáš Polách as club captain and signing a five-year deal with firm Fastav, replacing the former sponsorship deal with Tescoma to take the new name FC Fastav Zlín.
In May 2017 FC Fastav Zlín won their first major trophy in Czech League Cup called MOL Cup. Because simultaneously Manchester United won trophy in Europa League and Slavia Praha won Czech League, Zlin automatically qualified for the 2017/18 Europa League Group Stage. They will feature in group stage of any European Cup for the first time in their history.