Jokubaitis played for Lithuania at the 2016 FIBA U16 European Championship in Poland. He averaged 10 points and helped his team win a silver medal. Jokubaitis was the youngest player at the 2017 FIBA Under-19 World Cup in Egypt, averaging 10 points and 5.3 assists per game for the sixth-place team. At the 2018 FIBA U18 European Championship in Latvia, he averaged 12.9 points and 5.6 rebounds per game as his team finished fifth. Jokubaitis led Lithuania to fourth place at the 2019 FIBA Under-19 World Cup in Greece, where he averaged 11.3 points and 5.6 assists per game.