On February 15, 1995, Fujita debuted for the Japan national team against Australia. In June 1999, he was selected Japan for the first time in 4 years by manager Philippe Troussier. He played at 1999 Copa América. In 2001, he was selected Japan for 2001 Confederations Cup. Although he did not played in the match, Japan won the 2nd place. In October 2003, he was selected Japan for the first time in 4 years by manager Zico. In 2004, he played at 2006 World Cup qualification. He was also selected Japan for 2004 Asian Cup. Although he did not played in the match, Japan won the champions for 2 times in a row. He played 24 games and scored 3 goals for Japan until 2005.