After retirement, Ishii became a coach for Kashima Antlers in 1999. He served as mainly physical coach. In July 2015, manager Toninho Cerezo was sacked and Ishii became a new manager. He was the Japanese manager of the club for the first time in 21 years since Masakatsu Miyamoto in 1994 (Except caretaker Takashi Sekizuka in 1998 and 1999). In October, the club won the champions 2015 J.League Cup. In 2016, the club won the champions J1 League and qualify for 2016 Club World Cup. He was also elected J.League Manager of the Year. At Club World Cup, the club became the first Asian team to reach the Club World Cup final. In the final, after a 2–2 draw against European champions Real Madrid after 90 minutes, they were beaten 4–2 after extra time. However the club performance is bad in 2017, he was sacked in May 2017.