Fukunishi was born in Niihama on September 1, 1976. After graduating from Niihama Technical High School, he joined J1 League club Júbilo Iwata in 1995. He played as defensive midfielder with Dunga in 1990s. After that, he became a central player in golden era in the club history. The club won the champions at 1997, 1999 and 2002 J1 League. The club also 1998 J.League Cup and 2003 Emperor's Cup. In Asia, the club won the champions 1998–99 Asian Club Championship and the 2nd place 1999–00 and 2000–01 Asian Club Championship. He played 292 matches for the club until 2006. After that, he played FC Tokyo (2007) and Tokyo Verdy (2008).