The club was founded under the name PAL Jihlava in 1948. After the Czech Republic became independent in 1993, the club played in the third-tier Bohemian Football League until promotion in 2000 to the Czech 2. Liga. The club went on to take part in the second division for five years, reaching the semi-finals of the Czech Cup in 2003–04 and winning promotion to the top flight after finishing second in the 2004–05 Czech 2. Liga. Jihlava played in the top flight for the first time in their history in 2005–06, being relegated back to the second league on the last day of the season, after a loss at home against Slavia Prague. Following another spell in the second league, this time of six years, the club won back a place in the top flight having finished second in the 2011–12 Czech 2. Liga.
Jihlava play home matches at the Stadion v Jiráskově ulici, which boasts a 4,082 all-seater capacity. The club undertook major reconstruction each time the club was promoted to the Czech First League, in 2005 and 2012, in order for the stadium to meet league criteria. The stadium features two main stands for the crowd (sectors A and B), while the away fans are catered for with 229 seats behind one of the goals (sector D). The remaining side, sector C, is reserved for VIP guests.