Born in Belgrade, he played with the youth team of OFK Beograd until the season 2010–11 when he made his debut for the main team in the SuperLiga. On 29 August 2013, it was announced that Pavlovski signed for FC Porto on a one-year loan, with the Portuguese side having an option to buy out Pavlovski afterwards. His rights were in fact purchased by Apollon Limassol, who proceeded to loan him out to other clubs.
Marko Pavlovski has been member of the Serbian U19 team since 2011 and was a member of the Serbian squad at the 2012 UEFA European Under-19 Football Championship.
On 25 May 2013, Pavlovski received a call from Čedomir Janevski to represent Macedonia national football team on the friendly matches to be played on 3 and 11 June against Sweden and Norway respectively. He did not respond to this invitation. Months later, Pavlovski captained the Serbia U19 team that won the 2013 UEFA European Under-19 Championship.