St. Mary’s School was founded in the pioneer mining town of Jacksonville, Oregon, in 1865 by three members of the Sisters of the Holy Names of Jesus and Mary and was known as St. Mary’s Academy. Operating as a twelve-year (the upper grades were limited to girls) boarding and day school, it served pioneer families in Southern Oregon and Northern California. St. Mary’s graduated its first student in 1871.
St. Mary’s moved to Medford in 1908 and in the late 1920s became coeducational, graduating its first boy in 1930. In 1948 the Sisters of the Holy Names transferred title of the school to Sacred Heart Parish, which operated it as a twelve-year coeducational school for the next 13 years. In 1961 St. Mary’s Elementary and High School separated into two schools when the present High School was built on Black Oak Drive.
In 1971 when Sacred Heart Parish determined it could no longer financially support two schools, a group of supporters raised funds and gained permission from the Archbishop to incorporate as an independent Catholic school, the first in the state of Oregon. With the Archbishop’s permission, St. Mary’s added a middle school after a fire damaged Sacred Heart School and representatives of the parish and greater community asked the Board of Trustees to transfer the seventh and eighth grades to the school. A sixth grade was added in 1992.
In 1998 St. Mary’s began its first capital expansion in 31 years with a multi-phase building campaign. Since then, St. Mary’s has completed an expanded parking facility, an all-weather eight-lane track, upgraded athletic fields, and a library/media and science center with three science labs and seven additional classrooms. In 2012, a new Fine Arts & Athletic Center and St. Mary's Chapel were added to the campus.