In 2003, Konno was selected the Japan U-20 national team for the 2003 World Youth Championship. He played all 5 matches as defensive midfielder. In 2004, he was also selected the Japan U-23 national team for 2004 Summer Olympics and played all 3 matches. In 2005, he was selected the Japan national team for 2005 East Asian Football Championship. At this tournament, he debuted against China on August 3. He played at 2007 Asian Cup and 2010 World Cup. After the 2010 world cup, he became a regular player as center back under new manager Alberto Zaccheroni. In 2011, he played at 2011 Asian Cup and Japan won the champions. However his opportunity to play decreased behind Masato Morishige from 2013. He was selected Japan for 2014 World Cup and played 2 matches. After the 2014 World Cup, he played as midfielder under manager Javier Aguirre and Vahid Halilhodžić. He played 93 games and scored 4 goals for Japan until 2017.