Pušnik started his managerial career in 1994 but landed his first serious job as Celje manager in 2000. During his 4 years at Celje, his biggest success was in the 2002–03 season when his team finished second in the 2002–03 Slovenian PrvaLiga and runners-up in the 2002–03 Slovenian Football Cup. After a few years in Iran, he returned to Slovenia and took over Maribor in 2007 with whom he eliminated Villarreal CF in the UEFA Intertoto Cup but after the arrival of Zlatko Zahovič in the club, Pušnik was sacked. After a few years of working at Rudar Velenje where he managed to finish 3rd in the league after the club gained promotion, he returned to Iran again.
In 2015, Pušnik came to Olimpija Ljubljana where he gained most fame. He managed to build a strong side which dominated the first half of the season with attractive offensive football. He is notable for using and selling players such as Andraž Šporar and Ezekiel Henty. After dropping out of the Slovenian Cup, he fell into an argument with sporting director Ranko Stojić and was then sacked in December 2015. Olimpija went on to win the title that year.
On 2 June 2016, Pušnik was announced as the new manager of Hajduk Split and thus, he became the first Slovenian manager of Hajduk Split in history.