Jazz began to be taught at HAMU in 2011 thanks to the initiative of Professor Jiří Hlaváč, former dean of the school and a long-time supporter of jazz music in the Czech Republic. The head of first the Jazz Section and since the 2016/17 the independent Department of Jazz Music has been from the very beginning double bassist Jaromír Honzák, who years ago was also at the inception of the jazz studios at Jaroslav Ježek Conservatory.

During its first five years of existence, five main fields were set up (percussion, piano, double bass, guitar and saxophone), which can be studied at both the bachelor's and master's level. Regular instruction is supplemented by open workshops by primarily international artists, which have featured Maria Schneider, Doug Hammond, Kneebody, Adam Nussbaum and Jay Anderson, Rory Stuart, Antonin-Tri Hoang, Rudy Linka and more.

Every year the Jazz Department organises concerts for the public at HAMU featuring both student bands and extracurricular ensembles, as well as other foreign visiting lecturers. The culmination of the jazz season is the open-air festival "Jazz Courtyard", where all the student bands perform outdoors.