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".