Ishimaru was born in Katano on October 30, 1973. After graduating from Hannan University, he joined newly was promoted to J1 League club, Avispa Fukuoka in 1996. He became a regular player from first season and played many matches until 2000. In 2001, he moved to J2 League club Kyoto Purple Sanga. He played as regular player and the club won the champions and was promoted to J1 from 2002. In 2002, the club won the champions Emperor's Cup first major title in club history. In 2003, although he became a captain, the club finished at bottom place and was relegated to J2 from 2004. In 2005, he could not play at all in the match and moved to Japan Football League club Ehime FC in October. The club won the champions in 2005 and was promoted to J2 from 2006. He played many matches as substitute and retired end of 2006 season.
After retirement, Ishimaru started coaching career at Ehime FC in 2007. He served as coach for top team (2007–09) and manager for youth team (2010–12). In 2013, he became a manager for top team and managed the club until 2014. In 2015, he moved to Kyoto Sanga FC and became a coach. In July 2015, manager Masahiro Wada sacked and Ishimaru became a new manager as Wada successor. In 2016 season, the club finished at 5th place and missed promotion to J1. He was sacked end of the season.