After retirement, Yamamoto started coaching career at Yamaha Motors (later "Júbilo Iwata") in 1987. In 1995, he became a manager for Japan U-20 national team and managed at 1997 World Youth Championship. In 1997, he returned to Júbilo Iwata. In October 1998, he became an assistant coach for Japan national team under manager Philippe Troussier. After 2002 World Cup, in August, Yamamoto became a manager for Japan U-23 national team and managed at 2004 Summer Olympics. In November 2004, he returned to Júbilo Iwata and became a manager. He resigned in June 2006.