John Stephen Vaughan (24 January 1853 – 4 December 1925) was an English Roman Catholic bishop, brother of Bernard, Roger, and Herbert Vaughan.
He was son of Lieutenant-Colonel John Francis Vaughan, of an old recusant (Roman Catholic) family, the Vaughans of Courtfield, Herefordshire. His mother, Eliza Rolls from The Hendre, Monmouthshire, was a Catholic convert and intensely religious. All five of the Vaughan daughters became nuns, while six of the eight sons took Holy Orders and became priests. Three were later called as bishops: Roger became the Roman Catholic Archbishop of Sydney, Australia; Herbert, the eldest, became Archbishop of Westminster. John, in his turn was made the titular bishop of Sebastopolis and auxiliary bishop in Salford in 1909.
He was born at Courtfield, near Ross-on-Wye in Herefordshire, studied at St. Gregory's College, and at Bruges and Rome, and was ordained a priest on the 4 June 1876. Immediately after ordination he was appointed to the staff of the recently opened St. Bede's College as Professor of Mathematics, however he resigned in November of that same year following a breakdown in health and was invited by his brother Bishop Roger Vaughan to come and undertake Missionary work in Australia. He returned to England in July 1879 and rejoined the staff of St Bede's in his former role as Professor of Mathematics, where he remained until July 1886.
In 1886, Fr Vaughan was invited by his brother Fr Kenelm Vaughan to join him at his new venture 'The House of Expiation' in Chelsea, London. In 1896, he was appointed domestic prelate to the Papal Court with the title Monsignor and in 1898 became Canon of Westminster. Between 1890 and 1903, he organized free Catholic lectures in various public halls in London. He resided in Rome 1904-07, and then undertook a preaching tour in the United States and Canada.