His first work as a head manager was at FK Drnovice in 1986–1988, he then coached Hanácká Slavia Kroměříž and Tatran Poštorná.

For the next season he returned to the Czech Republic to work at Silesian club Baník Ostrava.

Baník led the league almost the whole 2003–04 season and won the Gambrinus liga for the first time in the history of the independent Czech Republic.

"[5] Afterwards Komňacký went back to Slovakia and won both the Slovak Cup and the Corgoň Liga with MFK Ružomberok in the 2005–06 season.

[6] In the summer of 2012, Komňacký left Jablonec after nearly five years in charge, joining Gambrinus liga newcomers Vysočina Jihlava.