His father, lieutenant John Francis Vaughan, belonged to one of the oldest recusant families of Welsh descent in England.

In 1855, at his father's request and expense, Vaughan was sent to Rome for further study under the guidance of the Italian scholar and reformer Angelo Zelli-Jacobuzzi.

He returned to Downside in August of the same year and in 1861 was appointed professor of metaphysics and moral philosophy at St Michael's, Belmont, Herefordshire.

[3][1] Vaughan arrived at Sydney on 16 December 1873 and immediately devoted himself to two important movements: the provision of education for Catholic children and the rebuilding of St Mary's Cathedral which had been damaged by a previous fire.

The consequences of the dissolution of the monasteries during the Reformation had left Vaughan deeply committed to the primary vision of restoring monasticism in English-speaking lands such as this new church in Australia.

This was not a vision the authors of the revived authoritarian devotional form of Catholicism in Ireland foresaw for the Irish Catholic diaspora in Australia, New Zealand or North America.

This was an ideological battle Vaughan fought through his episcopate, the outcome of which would not be largely determined until his successor Cardinal Patrick Francis Moran, a nephew of Paul Cullen and avid devotee of his vision, was appointed.

He arrived at Liverpool and died nearby at Ince Blundell Hall, the seat of his Weld-Blundell relations, on 18 August, where he was buried in the family vault.