The presence of La Salle in northern Mindanao came to be with the invitation of Msgr. Patrick Cronin of the Prelature of Ozamiz City to take over St. Columban's Academy in Iligan City. This was the same school that used to be Woodrow Wilson Junior College in 1947. The invitation was accepted in 1958. The school was located in downtown Iligan, a stone's throw away from the Cathedral. A growing student population and the need for a bigger campus led to the purchase of a three-hectare lot in Pala-o belonging to the estate of Pedro Nuñez. The transfer to the new site happened in 1960 which also saw the name of the school change to La Salle Academy.

In 1999, Br. Jaime Dalumpines FSC spearheaded the purchase of a property on Mt. Agad-Agad with the intention of using the property for recollections as well as developing it into an Ecology sanctuary. With the purchase came the adoption of a nearby purok, Langilanon, with the academy helping the town's farmers to establish the Langilanon Farmers Cooperative. It was also during this year that the Technical and Vocational Education Training Department was established.