FC Vysočina Jihlava was established in 1948 and initially operated under the name PAL Jihlava. Between 1953 and 1993, the team was known as Spartak Jihlava. The club adopted its current name in 2000. Historically, the side has spent most of its lifespan in the lower divisions of the Czechoslovakian and Czech Republic's respective league systems.
When the Czech Republic gained independence from Czechoslovakia in 1993, Vysočina Jihlava were entered into the Bohemian Football League; the country's third division. They remained in the league for seven seasons, before a second place finish in the 1999-00 season saw the club promoted to the Druhá Liga. After several years in this league, the club gained promotion to the top tier, the Gambrinus Liga, at the conclusion of the 2004-05 campaign. Their initial stay in the division lasted just one year and they were relegated on the last day of the season, after a defeat at the hands of Slavia Praha. At the end of the 2011-12 season, a 2nd place finish saw them return to the top flight once again.
To date, the club has failed to win major honours and none of the club's promotions up through the Czech league system have been the result of league wins. However, Vysočina Jihlava have performed relatively well in the Czech Cup. In 1995-96, despite playing third tier football, they reached the quarter final stage of the competition. Then, in 2003-04, whilst playing in the second division, they went one better and reached the semi finals.
The team currently play their home matches at the Stadion v Jiráskově ulici. After gaining promotion in 2005, the stadium underwent renovations to bring it in line with the standards required for a top flight venue. This work included the installation of floodlights and an expansion of the ground's capacity. It is currently able to seat up to 4,082 supporters.