The school was built by Mill Hill missionaries to spread Catholicism among the local Kadazan-dusun community, who were mostly animists.
With the establishment of Malaysia on September 16, 1963, the school's educational ethos gradually transitioned towards a more secular approach.
As a result, the present day St. Michael's church and the school were built in Kampong Dabak, Penampang, which was close to this river.
The initial school structure, constructed from bamboo, served as both a classroom and residence for the church's priests.
SM St Michael fostered a relationship with Yong-ho High School, South Korea and ended their participation in the KDCA-ISEP exchange program.
They dubbed the relation a sisterhood and organised an English Camp for South Korean students who arrived in Sabah in July 2008.