After the retirement, Sekizuka became an assistant coach for Kashima Antlers under manager Masakatsu Miyamoto in 1993. In 1995, he moved to Shimizu S-Pulse with Miyamoto. In 1996, he returned Kashima and coached until 2003. In July 1998 and August 1999, he also managed the club as caretaker manager. In 2004, he moved to J2 League club Kawasaki Frontale and became a manager. In first season, he led the club to the champions and the club was promoted J1 League. In April 2008, he resigned for health reasons. In 2009, he returned the club as manager, but he resigned end of the 2009 season. In September 2010, he became a manager for Japan U-23 national team for 2012 Summer Olympics and an assistant coach for Japan national team. At 2012 Summer Olympics, he led Japan to the 4th place. From 2013, he managed Júbilo Iwata (2013) and JEF United Chiba (2014-2016).