He had previously coached FK Vardar, FK Sloga Jugomagnat winning three championships and one cup title. After FK Rabotnički Kometal winning two championship and qualified in the third round qualification for UEFA Champion League (eliminated by Lille/France)before moving to FK Milano Kumanovo and FK Metalurg Skopje. He was also a Head coach of Macedonian national team from 2001 till 2002. He was chosen three times for the award of the "best football coach in Macedonia" by Sport radio 90.3 fm having been one of the best coaches in Macedonia winning five league and two cup titles. He was also the head coach of the Macedonian national team from 2001 to 2002.
On 8 November 2011, Jovanovski was named as manager of FK Rabotnički but after only two months as the manager, the club board and he agreed to mutually terminate his contract on 28 December 2011.