St. Raphael's Parish, the predecessor body to Mary Queen of Peace Parish, was founded in 1924 to serve a Catholic population then living on the outskirts of St. John's. Throughout its existence, the parish used St. Raphael's Chapel, located in Mount Cashel Orphanage, as its centre of worship church (the pastor of St. Raphael's also acted as the chaplain for the Irish Christian Brothers, operators of the Orphanage). However, in 1963, Mary Queen of Peace Parish was erected to serve the growing northeast area of St. John's. A school-chapel complex was constructed on Torbay Road to serve the needs of the new parish. Alphonsus L. Penney, Archbishop of St. John's, offered the first mass there on 23 February 1964. On the same day, St. Raphael's Parish was officially suppressed and superseded by Mary Queen of Peace. St. Raphael's Chapel thus reverted solely to the use of the Irish Christian Brothers and the boys of the Orphanage. The new Mary Queen of Peace School also replaced St. Raphael's School (more popularly known as Bally Haly School) after its closure in June 1963.

Initially, Mary Queen of Peace Parish was served by priests from the Basilica Parish because of a shortage of clergy in the Archdiocese of St. John's. However, permission was granted to build a presbytery in 1966, marking a permanent clerical presence within the parish.

The school-chapel complex served Mary Queen of Peace Parish until it was destroyed by fire in October 1982. After the fire, religious services were held in the Parish Hall on Macdonald Drive until a new church was built on Torbay Road. The first mass was said in this new structure in December 1984 and it was later blessed and dedicated by Archbishop Penney on 21 June 1985. A new Mary Queen of Peace Elementary School also was built on Torbay Road.

The Mary Queen of Peace Parish Pastoral Council (as of 1 January 1989) was comprised of 21 members, including the pastor and associate pastor, laity, and representatives from parish groups. Headed by the pastor, the Parish Pastoral Council manages the activities and affairs of Mary Queen of Peace.

In 1987, an organizational committee was established to investigate a more effective committee system for Mary Queen of Peace Parish. Its recommendations led to the creation of four sub-committees (also called ministries or commissions) responsible for carrying out the policies of the Parish Pastoral Council: Administration, Liturgical, Education, and Christian Service. A fifth sub-committee, Outreach, was later added. The chairmen of these five major sub-committees were selected from the Parish Pastoral Council and were responsible for reporting to the Council on the activities of various committees, organizations, and societies operating within their sphere of functional responsibility. The number of active parish committees are discretionary and are meant to be flexible to accommodate changing needs and priorities. Therefore, the number and types of committees are constantly evolving.

Pastors who have served St. Raphael's and Mary Queen of Peace parishes include: Thomas Bride (1924-1951); William Lawton, Administrator (1951); Francis J. D. Ryan (1952-1964); Michael T. Connolly, Administrator and later Parish Priest (1965-1977); Eric R. Lawlor (1977-1984?); Charles Kelly (1984?-1989); John Wallis (1989?-1994?); Allan Farrell, Co-Pastor (1999-2001); and Gerard Whitty, Co-Pastor and later Pastor (1999- ).