On March 24, 1999, when Kobayashi was 17 years old, she debuted and scored a goal for the Japan national team against France. She was a member of Japan for 1999, 2003 World Cup and 2004 Summer Olympics. She also played at 2001, 2003 AFC Championship and 2002 Asian Games. She played 54 games and scored 12 goals for Japan until 2004.