CIS was founded in 1999 by two of its present directors. Contact was established with the Department of Education of the Canadian province of Prince Edward Island to adopt that province’s curriculum at Canadian International School Tokyo (CIS). CIS is accredited annually with an onsite inspection by officials from the Department of Education in Prince Edward Island.

CIS is an accredited pre-kindergarten to grade twelve Canadian school. CIS received final authorization for the International Baccalaureate Primary Years Program (IB PYP) in 2009. In Japan, CIS is recognized by the Japanese Ministry of Culture, Sports, and Education, so CIS high school graduation is recognized for those students who apply to enroll in Japanese universities. CIS is a member of the Japan Council of International Schools and the Tokyo Association of International Preschools.