On July 31, 1990, Nakayama debuted for the Japan national team against North Korea. In 1992, he was selected the Japan for 1992 Asian Cup which held in Japan. He scored 2 goals in the tournament and Japan team won the champions. In 1993, he played at 1994 World Cup qualification in Doha. However Japan failed to qualify for the 1994 World Cup. It was known as the "Agony of Doha" () in Japan. In November 1997, he scored 2 goals for Japan during 1998 World Cup qualification final round and playoff, leading the Japan to their first ever World Cup. At the 1998 World Cup, Nakayama scored the only goal of the tournament and the first goal for Japan in the history of the World Cup against Jamaica on June 26. He also played at 2001 Confederations Cup and 2002 World Cup which held in Japan. He played 53 games and scored 21 goals for Japan until 2003.