Endo was born in Kagoshima on January 28, 1980. After graduating from Kagoshima Jitsugyo High School, he joined J1 League club Yokohama Flügels in 1998. In March, he debuted against Yokohama Marinos in opening game in 1998 season. He played many matches as central midfielder in 1998 season. The club won the champions in 1998 Emperor's Cup. However the club was disbanded end of 1998 season due to financial strain. In 1999, he moved to Kyoto Purple Sanga with contemporaries Kazuki Teshima, Hideo Oshima and so on. He became a regular player and played many matches. However the club was relegated to J2 League end of 2000 season.
In 2001, Endo move to J1 club Gamba Osaka. He played as central player for the club for long time under manager Akira Nishino (2002–2011). He was also selected J.League Best Eleven for 10 years in a row (2003-2012). In 2005, Gamba won the champions in J1 League first time in the club history. In 2008, Gamba won the champions in AFC Champions League for 2 years in a row as Japanese club (Urawa Reds won in 2007). Gamba also won the 2008 Emperor's Cup. Endo was selected "Japanese Footballer of the Year". In 2009, Gamba won the Emperor's Cup for 2 years in a row. Endo was selected "Asian Footballer of the Year".
However manager Nishino left Gamba end of 2011 season and the club performance deteriorated soon. In 2012, Gamba finished at the 17th place of 18 clubs and was relegated to J2 League. Gamba won the champions in 2013 season and returned to J1 in a year. In 2014 season, Gamba won all three major title in Japan, J1 League, J.League Cup and Emperor's Cup. Endo was selected "J.League MVP" first time and "Japanese Footballer of the Year" second time. Although he played as regular player for a long time, his opportunity to play decreased in 2020. In October 2020, he moved to J2 League club Júbilo Iwata.
In April 1999, Endo was selected the Japan U-20 national team for 1999 World Youth Championship. At this tournament, he played all 7 matches as defensive midfielder and Japan won the 2nd place. On November 20, 2002, he debuted for the Japan national team against Argentina. After the debut, he became a regular player. In 2004, he played at 2004 Asian Cup and Japan won the champions. However he lost his position from 2005. In 2006, although he was selected Japan for 2006 World Cup, he could not play in the match.
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.
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