On 2 February 2011 it was announced that Ajax Amsterdam had acquired the young left back from the Swiss club on a 3-year contract lasting until 1 July 2014. Already a member of the Switzerland U-17 national team at age 16, Ajax won the young player over ahead of Juventus, Sampdoria, Brescia, Nancy and Valenciennes, all who were in running for the young defender. Joining the Ajax B1 squad at first, Stefan worked his way up the youth ranks even playing in the Beloften Eredivisie for the reserves team Jong Ajax during the 2011–2012 season. On 28 January 2012, in a match against ADO Den Haag reserves that Stefan Marinković suffered a severe injury. Sidelined for an entire season, it wasn't until the 2013–2014 season, that he made his professional debut on 30 August 2013 playing for the reserves team Jong Ajax against Jong Twente in the Dutch Eerste Divisie, the 2nd tier of professional football in the Netherlands. The match ended in a 2–1 win for Jong Ajax, with Marinković coming on in the 77' minute for Derwin Martina.
