At the youth level, Alibegović played for the Yugoslavia Under-18 and Under-19 national teams, which won the 1986 FIBA Europe Under-18 Championship, and the 1987 FIBA Under-19 World Cup. Alibegović was a member of the senior men's Slovenian national basketball team, from 1991 to 2001. With Slovenia, he played at four EuroBaskets (1993, 1995, 1997, 2001). With Slovenia's senior national team, he played in 52 games, and scored 990 points, which made him the all-time top scorer of Slovenia's senior national basketball team.