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Znojmo won promotion from the Czech Fourth Division in 2002, finishing first in Division D in the 2001–02 season. The club followed this with eight seasons in the Moravian–Silesian Football League, before winning another promotion in 2010 under manager Michal Sobota. The club secured promotion to the Czech 2. Liga two matches before the end of 2009–10 season. Znojmo replaced Sobota in the summer of 2010, partly due to him not having a coaching license for professional football. His replacement was Bohumil Smrček.

Two relatively unsuccessful seasons followed under Smrček, with the club finishing 14th and 13th respectively. This prompted the club to replace Smrček with new manager Leoš Kalvoda. Kalvoda went on to lead the club to a first-place finish in the 2012–13 Czech 2. Liga and Znojmo celebrated promotion from the Czech 2. Liga, winning the right to play in the top flight for the first time in their history. They finished bottom of the 2013–14 Czech First League, and played all of their matches in Brno (aside from one which was played in Jihlava) due to their own stadium not meeting league requirements.

Historical names

• 1953 – DSO Rudá Hvězda Znojmo
• 1969 – TJ Rudá Hvězda Znojmo
• 1990 – SKP Znojmo-Práče (after incorporation of TJ Sokol Práče)
• 1992 – SKPP Znojmo
• 1993 – VTJ SKP Znojmo
• 1994 – VTJ Znojmo-Rapotice (after incorporation of TJ Sokol Rapotice, 1997 Sokol Rapotice split again)
• 1995 – VTJ Znojmo
• 1999 – Fotbal Znojmo
• 2001 – 1. SC Znojmo FK (after incorporation of FC Znojmo)