Prepelič took part in the 2012 FIBA Europe Under-20 Championship with Slovenia. He posted a double-double of 20 points and 11 assists against eventual champion Lithuania in the first round, 29 points and 4 assists against Turkey in the second round, and 17 points against France in the quarterfinals. He was included in the All-Tournament Team. Prepelič debuted for the Slovenian national basketball team at the 2014 World Cup. He also represented Slovenia at the EuroBasket 2015 where they were eliminated by Latvia in eighth finals.