Prkačin was a member of the Croatian Under-22 junior national team. His debut at a major tournament with the senior Croatian national team's selection came at the 1997 EuroBasket. After that, he played with Croatia at the following major FIBA tournaments: the 1999 EuroBasket, the 2001 EuroBasket, the 2003 EuroBasket, the 2005 EuroBasket, and the 2007 EuroBasket, He also represented Croatia at the 2008 Summer Olympics and the 2009 EuroBasket. Prkačin was Croatia's team captain twice.