After graduating from Kagoshima Jitsugyo High School, he joined J1 League club Yokohama Flügels in 1998.

Due to financial strain, the club was disbanded at the end of the season and merged with Yokohama Marinos.

In 1999, Endō moved to Kyoto Purple Sanga with contemporaries Kazuki Teshima and Hideo Oshima.

[8] Endō played in the 1999 World Youth Championship and Japan finished as runner-up, losing to Spain in the final.

On 24 June 2010, Endō scored from a free kick against Denmark in a 3–1 win as Japan qualified for the second round of the World Cup.

[10] On 12 October 2010, he became the fourth player to earn a 100th full international cap for Japan in a friendly match against South Korea.

[11] His start in this match was his 123rd appearance for the national team, surpassing Masami Ihara's previous record of 122 caps.

[11] Endō was included in Japan's squad for the 2015 Asian Cup and scored the team's opening goal of the tournament in a 4–0 defeat of Palestine.

He is also known for his excellent accuracy on free kicks and is revered as one of Japan's most creative midfielders as well as one of the most talented Japanese footballers and playmakers of his generation, this despite only playing domestically in his home country.