SJI consists of a primary school and a secondary school. The primary and secondary schools initially were fee paying missionary schools and remained as such until the 1970s. They functioned together until the increase in enrolment of pupils led to a separation of the primary school in 1960. The primary schools are formally known in Malay today as "Sekolah Kebangsaan St. John (1)" and "Sekolah Kebangsaan St. John (2)" while the secondary school was called "Sekolah Menengah Kebangsaan St. John", but it was announced in April 2016 that the name would be reverted to St John's Institution, a decision widely applauded by alumni and backed by another Johannian Sultan Nazrin Shah of Perak.