The history of St. Mary's College, Quezon City may be traced back to the foundation years of the congregation which started one of the first exclusive schools for the girls in 1725. A landmark in Spanish Intramuros, it was known as the Colegio del Beaterio. The "beatas" taught not only catechism but also fancy needlework for this was their main source of support. After several years, they started to teach the Spanish language and the fundamentals of proper home management. The teaching of social graces followed. Among the popular subjects of the old Beaterio were fancy needle work and music.

The Institution became more formally organized through the years, in 1901; the Beaterio held its first general chapter and became a congregation. Eleven years after, in 1912 the school was formally incorporated and the elementary Course was recognized by the government. The high School was opened and duly given recognition shortly after. Domestic Science, now known as Home Economics, was formally offered making the college one of the first private schools to offer such course. The school received in 1935 the formal government recognition of Junior Normal College course. In 1939, the name Colegio del Beaterio was officially changed to St. Mary's College in honor of the Blessed Virgin Mary, the Patroness of the Congregation. In the same year, the Bachelor of Science in Education was formally recognized by the government. Since then, other college courses began to be offered.

St. Mary's College was the first private school to open its doors just after the liberation of Manila in 1945 in answer to the needs of students who wanted to resume or finished their studies. Originally established for girls, St. Mary's College admitted boys in the Grade School after the war.
Since the building in Intramuros has been reduced to ashes, its site was transferred to the Immaculate Conception Ladies Hall in España, just in front of the University of Santo Tomas. From 1946 to 1950, however, it was housed in a rented building at Aragon Street, Sampaloc. In April1950 St. Mary's College made Quezon City its permanent site undaunted by the isolation of the place and the difficulty of transportation then.

College course offerings since 1950 included BSE, ETC, Secretarial, Associate in Arts, Bachelor of Music, Associate in Music, BSEED and other special courses. In 1976, the changing political, socioeconomic and cultural climate led the administrators to temporarily suspend the college. There was also a felt need to concentrate on basic education. In its desire to upgrade the equality of instruction, St. Mary's College embarked on a self-evaluation project which led to a formal application for accreditation through the Philippine Accrediting Association for Schools, Colleges and Universities (PAASCU). The High School department was accredited in 1975 and the Grade School department in 1978. Subsequently PAASCU visit confirmed the quality education offered by St. Mary's College. In 1997, St. Mary's College heeded the request of parents to admit boys to High School. With the continuing improvement in its instruction and services, The Board of Trustees thought it was time to resume the college. Preparations were done and in 2002, St. Mary's College was given the permit to start offering a Bachelor's Course in Communication Studies.

True to its tradition, St. Mary's College, Quezon City believes firmly that the home is the essential element in society and most influential factor in most aspects of human development. The institution is committed to carry on a strong program of religious instruction, communication and social services.