Flores represented Argentina at various youth levels. He was a part of the squad that won the 2017 South American U-15 Championship, with the centre-back scoring a goal during a draw with Chile on 11 November. Two years later, Flores made seven appearances as they won the 2019 South American U-17 Championship in Peru. At the subsequent FIFA U-17 World Cup, Flores scored a goal against Cameroon. He also featured at numerous friendly tournaments at youth level, as well as appearing in U17 friendlies with the United States and, scoring against, New Zealand. In December 2020, Flores received a call-up from the U20s.