Following the resignation of Sir John Kirwan, Jones was appointed in 2012 as head coach of the Japan national rugby union team, to lead them to the 2015 Rugby World Cup. He quickly took the team in a different direction from Kirwan. His first move as the Japan coach was to reduce the number of foreign players, who had been a prominent part of the Japan team under Kirwan, and to encourage the Japanese to play their own style. He also said his goal was to bring Japan up a level, to be among the top 10.