The establishment of EISJ in April 2013 came as a culmination of years of effort and desire of Nepalese community in Japan to establish a Nepalese curriculum based school that could cater to the educational needs of the Nepalese children growing up in Japan. The need for the establishment of the school was felt in the backdrop of rapidly increasing Nepalese population in Japan and the corresponding need to provide English medium education to the students.

In order to open and operate the school in Japan, Non Profit Organization Nepal Education Center, Japan was established in December 2012. The school was officially started in April 2013 under the management of Nepal Education Center, Japan. The initial funding for the establishment of school was contributed by the the members of Nepali community in Japan.

Ministry of Education of Nepal Government formally endorsed the operation of school in March 2015. Everest International School, Japan is the only school being operated outside Nepal using the English medium Nepalese curriculum.