La Sallian Brothers

The school was founded by the La Sallian brothers and as such, has traditionally been headed by a brother. The headmaster of the school was a Brother Director while a Brother Supervisor acted as deputy headmaster. In recent years, the post of Brother Supervisor was replaced with two assistant principals, both not of the order.

One of the more famous Brother Directors is Brother Datuk Lawrence Spitzig, who also served two terms as Brother Director of St. John's Institution, Kuala Lumpur. He served in SXI from 1960 - 1967.

With the retirement of Brother Paul Ho, the last of the La Sallian Brother principals, on 19 June 2009, the school will be helmed by a government-appointed layperson, although Brother Charles Levin remains as Brother Director. St. Xavier's Institution was one of the last remaining missionary schools in Malaysia to be led by the missionaries and, certainly, the last in Penang.

A board of governors was formed in 2008 to oversee the school upon the retirement of Brother Paul.

Two brothers remain resident in St. Xavier's, although not officially part of the school proceedings.