Endo made his debut for Japan against Italy in July 2004, but then had to wait until 2006 until he returned for his second cap and then established himself as the first choice right wing after Daisuke Ohata late career was plagued by injuries, and remained there for most of John Kirwan's time as Japan coach between 2007 and 2011.
In the 2007 Rugby World Cup he notably finished a spectacular break out try from their own 5 metre line against Wales at the Millennium Stadium which was praised as one of the outstanding tries of the tournament one of Japan's best of all time. He followed that up by scoring another try against Canada in the next match from a run just under 50 metres through the defence. Endo left the World Cup with an increased reputation and coach John Kirwan said that "he could be one of the best wingers in the world". In 2008, Endo signed to play a season in the Air New Zealand Cup with Canterbury.
Endo remained in the Japan side up until the 2011 Rugby World Cup where he started 3 matches. In the last match against Canada, Endo again scored a try like he did against the same opposition in the 2007 tournament, but also had a nightmare match in defence missing 5 tackles one of which led to a Canada try.