Zupan began his career with Zadarkomerc in the Croatian First Football League in 1995, where he would spend a total of four seasons appearing in 66 matches and recording one goal.

In 2003, he went abroad to Canada to sign with Toronto Croatia of the Canadian Professional Soccer League.

[7][8] He helped Toronto finish second in the International Division, and featured in the playoff quarterfinal match against the Laval Dynamites.

[11] In the semi-finals Croatia faced archrivals the Serbian White Eagles, where in the first match he scored a goal in a 3-1 defeat.

In 2011, he signed with SC Toronto, and helped the club win the regular season championship by finishing first in the overall standings.