Banega came through the youth ranks at Boca Juniors and it was not until he moved to the first team that he won international recognition, thanks to his impressive passing average and his excellent performances in the local league. After Boca midfielder Fernando Gago moved to Real Madrid, Banega was named as his successor despite his young age
He made his professional debut in the 4-0 victory against Banfield on February 10, 2007. On April 2, 2007, just a few matches after making his debut, he was given an ovation when he left the field
Banega helped the Under-20 National Team to win the 2007 FIFA U-20 World Cup in Canada, where his performances earned him much praise.