The school opened in 1978. Historically the school was located on the property of a local Australian school, and the two schools had joint activities. Since 1998 the school uses the four term system used by Australian schools.
The school was previously in Scarborough. In its history, up to 2012, the school had moved three times with its final location purported to be at City Beach. However, Education Minister Peter Collier announced that the Japanese School in Perth will be relocated  for the fourth time. The next location has not been disclosed.