A period of growth followed until 1907, when McLoughlin Institute, serving children up to tenth grade, was opened. The building, designed to accommodate 300 students, was three stories tall and featured a hall and gymnasium. St. John's Parochial and High School continued to serve as an annex for the new school.

In time, as Oregon City's population began to shift to the hilltop area, a program to finance the purchase of a piece of property and erect a new school on the hill was developed. In 1947, this goal was realized when the old school was razed and construction began. The new, fireproof school that is now St. John the Apostle Catholic School was completed and dedicated in 1948. A large basement, intended ultimately as a parish hall, was used as a temporary church until 1957.

For almost its first full century, the school was operated under the dedicated tutelage of Benedictine sisters. Their service continued until 1982, when school operations were passed entirely to the laity. Our current school boasts an academic program built on the early Benedictine tradition, which is now guided and directed by the Archdiocese of Portland in Oregon and the Catholic Schools Department. St John the Apostle Catholic School is accredited by the Northwest Association of Schools, Colleges and Universities (NASCU) and the Western Catholic Education Association (WCEA), ensuring that all state of Oregon educational standards and benchmarks are met and surpassed.