The College identity has been evolving over many years. Originally the current St Raphael's and St Paul's Wings were managed as two separate Colleges - St Raphael's for young women and St Paul's for young men (until St Paul's became co-educational in the 1980s). It is only in recent times that the two Colleges combined to form one.
St Raphael's College for women was established under the auspices of the Roman Catholic Bishop of Townsville. The College patron is the Archangel Raphael who is portrayed in the Scriptures as the agent of God's loving care who brings the young Tobias and Sarah to the freedom of a fulfilled and happy life.
Members of the Grail, an international Christian lay women's movement, which is particularly concerned with the contribution of women to the renewal of Church and society, conducted the College.
St Paul's College commenced by the Roman Catholic Diocese of Townsville as an all male residential College. The initial administration was carried out by Franciscan Friars who conducted the College for a period of twenty-one years. After that time St Paul's College was managed by a series of religious as well as lay Principals.
O'Leary Wing (A Block) was named in honour of Dr Gerry O'Leary, a Townsville dentist and member of the St Paul's College Council. Dr O'Leary was supportive of Catholic initiatives within the Diocese and was a prominent advocate in the vision to establish St Paul's College.
Kneipp Wing (B Block) was named in honour of Sir Justice George Kneipp, a prominent Townsville figure, Chancellor of James Cook University and long serving Chair of St Paul's College Council in its early years.
The Merrick Wing was named in honour of the College's founding Principal, Miss Moya Merrick, and the original wing was named the Grail Wing in honour of the significant contribution of The Grail.
St Paul's College became co-educational, and has operated in this capacity ever since.
St Raphael’s College has been conducted by religious as well as lay Principals.
In September of this year, The Most Rev. Bishop Michael Putney, D.D., Bishop of Townsville, approved the combining of the two Catholic Colleges which were to be administered jointly and known as The Combined Catholic Colleges of St Raphael and St Paul and operating within the framework of The Roman Catholic Trust Corporation for the Diocese of Townsville.
St Raphael's College combined with St Paul's College to become The Combined Catholic Colleges of St Raphael and St Paul.
The College underwent another name change to become The Catholic College of St Raphael and St Paul.
A new co-educational wing was built and added to the College. The building was named St Mary MacKillop Wing in honour of Australia's first saint, St Mary of the Cross MacKillop.
Bishop Michael Putney officially approved the renaming of the College to Saints Catholic College. This change was necessary to better reflect the College's inclusive identity. At the same time, Bishop Putney approved a new Crest for the College which combined various aspects of the two former crests and added new elements as well.