Pušnik started his managerial career with Dravograd in 1994 but landed his first serious job as Celje manager in 2000.

After a few years in Iran, he returned to Slovenia and took over Maribor in 2006 with whom he eliminated Villarreal in the 2006 UEFA Intertoto Cup.

[1] After a few years of working at Rudar Velenje, where he managed to finish third in the league, he went back to Iran.

[2] After Olimpija finished the first part of the season as the leading team in the league, Pušnik fell into an argument with sporting director Ranko Stojić and was sacked in December 2015.

[6] On 9 March 2017, Pušnik returned to Olimpija Ljubljana, replacing Luka Elsner.