The school has traditionally been headed by the Brothers of the
La Sallian order, with a Brother Director (like a headmaster) and a Brother Supervisor (like a deputy headmaster). In recent years, the Brother Supervisor was replaced with three assistant principals, who are not in the La Sallian order.
Former Brother Director of St. John's Institution The headship of the school passed to the laity in 2002 when Peter Yii Sing Chiu became the first non-brother and non-Catholic to head the school. Ending 98 years of Brothers' administration.
Former and Current Principals of St. John's Institution Brothers who have served as primary school headmasters since leaving the secondary school include Brother Patrick Arokiasamy, Brother Alban Tang and Brother Matthew Liew. On 1 December 2009, Mr. Peter Yii Sing Chiu was replaced by Mr. Leong Kum Loy. Under the administration of Mr. Leong Kum Loy, St. John has been declared a Heritage Site by the Malaysian government. The administration of this school has been continued until now by Mr. Sivakumar a/l Thannimalay, the seventh principal of SJI who has started serving from January 2023. He is assisted by three senior assistants as follows; • Senior Assistant of Administration and Curriculum: Datin Rohani binti Jusoh • Senior Assistant of Student Affairs: Mr. Musannef bin Yatim • Senior Assistant of Co-Curricular Activities: Mr. Eza Hamni bin Mohammad • Senior Assistant of Form Six: Madam Sharimala a/p Bahsu ==History==