After the 2006 World Cup, Endo became a regular player as offensive midfielder under new manager Ivica Osim and wore the "number 7" shirt for Japan as Hidetoshi Nakata successor. In 2008, Takeshi Okada became a new manager, he played as defensive midfielder with Makoto Hasebe. He was selected Japan for 2010 World Cup. He played all 4 matches and scored a goal from a free-kick against Denmark in a 3–1 win as Japan qualified for the knockout stage. In 2011, he played at 2011 Asian Cup and Japan won the champions. From autumn 2013, his opportunity to play decreased. He also played at 2014 World Cup and 2015 Asian Cup. He played 152 games and scored 15 goals for Japan until 2015.