The Sisters of Mercy from the Sacred Heart Convent in Cedar Rapids, Iowa came to Kalispell to open the school in 1917.

The school began as a combination convent and school with boarders, grades 1-9. Grades 10-12 were added within the first four years.

The high school was discontinued in 1941. St. Matthew's Parish bought the school and property from the Sisters of Mercy in 1956, and built a new building on the site. In 1958 St. Matthew's School began in the new building, which still houses the school today.

In 1970 the people of the parish found it necessary to close the eighth grade, and in 1974, the seventh grade was closed. Kindergarten was added in 1976, and preschool classes were added in 1982.