Jelić joined MŠK Žilina in the summer of 2013. On 28 July 2013, he scored a goal on his competitive debut for Žilina in a 3–1 league victory over FC ViOn Zlaté Moravce. In the 2014–15 season, Jelić became the league's joint top scorer (alongside Jan Kalabiška) with 19 goals. Overall, he scored 29 goals for MŠK Žilina in 68 league appearances, he also added 7 goals in the qualifying rounds of the UEFA Europa League.
SK Rapid Wien
On 31 August 2015, official website of MŠK Žilina announced departure of Matej Jelić to Austrian side SK Rapid Wien. He signed a four-year contract until the summer of 2019.