Sigma Olomouc traces its roots back to 1919, when it was founded in Olomouc as FK Hejčín Olomouc, taking its current name only in 1996 after a series of changes tied to its sponsors, including the industrial company Sigma that gave the club its lasting identity. Sigma reached the Czechoslovak First League for the first time in 1982-83, and after coach Karel Brückner took charge became a permanent member of the country's top flight from 1984, finishing third in the league on several occasions during the 1990s and early 2000s and runners-up in 1995-96.
It was during Brückner's era that Sigma produced its most celebrated result in European competition. In September 1999, in a UEFA Cup second-round tie, the club beat Turkish side Fenerbahçe 7-1 in the second leg to win the tie 7-2 on aggregate, before being eliminated in the next round by Juventus. In terms of how far the club advanced, however, Sigma's best European run came earlier, in the 1991-92 UEFA Cup, when the team reached the quarter-finals, still its furthest advance in a major European competition. That campaign also included a memorable meeting with Real Madrid, in which an 18-year-old Radoslav Látal became known as the "youngest libero in Europe" after Brückner trusted him with a starting role.
Domestically, Sigma's first major trophy came only in 2011-12, when the club won both the Czech Cup and Czech Supercup, an achievement followed by relegation from the top flight in 2014 and an immediate return the following season after winning the second division. In the 2024-25 season, Sigma added a second Czech Cup, beating Sparta Prague in the final and securing qualification for European competition.
Nicknamed Hanáci, after the surrounding Haná region of Moravia, Sigma play their home matches at the Andrův stadion in Olomouc, and remain, alongside Baník Ostrava, one of the leading representatives of Moravian football in the modern Czech league system.