Catholic education began in Coffs Harbour in 1913 when the Good Samaritan Sisters opened a school with 31 pupils. In 1972, the Sisters of Mercy of Grafton took over the running of St Augustine's School with the assistance of lay teachers.
After many years of planning by the Parish Priest of Coffs Harbour, Father Anthony Casey, and the Parents' Planning Committee, St John Paul College (originally called John Paul College) opened in 1983 for students in Years 7 and 8.
Land on Hogbin Drive was donated by Mr Paddy Hargraves, and the first stage of construction was completed in 1982. During that year, the original staff of 15 was appointed, and John Paul College was the first school in the Lismore Diocese to be opened with a lay Principal, Mr Peter Mullane. The Sisters of Mercy, Grafton, sent Sr Margaret Boyle as the Religious Education Co-ordinator. In recognition of the Mercy Sisters' input into the College, the College has a sports house named after their foundress, Catherine McAuley. Other houses are named after Fr Casey, the Parish Priest of Coffs Harbour, Mr Paddy Hargraves and Fr John Kelly, the Parish Priest of Sawtell at that time.
To commemorate the contribution of the Sisters of Mercy to St John Paul College, 1983 - 1992, the library has been dedicated to Catherine McAuley, their foundress.
The first Chaplain for St John Paul College was Fr Peter Slack from the Coffs Harbour Parish.
In 2014, after the canonisation of Pope John Paul II, the college was renamed St John Paul College.