The church was foundered by Rev'd Edward Stuart, the curate of Christ Church Albany Street. In the 1840's Mr Stuart, inspired by the Oxford Movement and the teachings of Pusey and Keble, approached the Bishop of London, with money Christ Church had raised, and offered the money and his ministry for the building of a new church in London. The Bishop decided on Munster Square, having the worst reputation in the city at the time for prostitution and poverty, not helped by the nearby Cumberland Barracks.
The architect R.C. Carpenter was tasked with building "a church as near perfection as the handicraft of man, the skill of architects and the experience and ingenuity of ecclesiastical art could make it". Alongside its beauty the vision for the church was for it to be free and open to all comers, that everyone might have an opportunity of worshipping God.
On July 15, 1849 the foundation stone was laid. A service of Holy Communion was celebrated in Christ Church. The services was fully choral, with the choirs of St Andrew's Wells Street, Margaret Chapel, St Mark's College, the boys of the Chapel Royal, St James' and the regular choir of Christ Church providing the music. The Rev. John Keble preached the sermon. After the Service, a procession was formed to proceed to the site, consisting of about seventy surpliced Priests and a surpliced Choir of eighty, followed by the greater part of the congregation. Keble hinted that troublemakers might be encountered and begged the congregation to "go reverently... as we pass through the streets of Babylon".
On April 22nd, 1852, the Church of St. Mary Magdalene was consecrated by Bishop Blomfield, and the following, in the handwriting of Mr. Stuart, is the earliest entry from the Parish Book :—
"The Right Rev. Lord Bishop of London consecrated the Church of St. Mary Magdalene on this day. Messrs. Holland and Charrington, parishioners of the new District Parish, with the Rev. Edw. Stuart, Perpetual Curate, presented the petition for consecration.
"The Prayers were said by the Rev. E. Stuart; the Lessons were read by the Rev. M. Shaw, and Rev. W. F. Powell, of Cirencester. The Epistle was read by the Rev. W. F. Burrows, and Holy Communion was administered by the Bishop, assisted by the Rev. E. Stuart, Rev. W. F. Burrows, and Rev. J. W. Molyneux, Assistant Curate of St. Mary Magdalene's, to 300 communicants.