Herbert Vaughan was born at Gloucester, the eldest 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 received Holy Orders and became priests. Three were later called as bishops in addition to Herbert: Roger became Archbishop of Sydney, Australia; Francis became Bishop of Menevia, Wales; John became titular bishop of Sebastopolis and auxiliary bishop in Salford, England.

In 1841 Herbert Vaughan, the eldest, went to study for six years at Stonyhurst College, then to the Jesuit school of Brugelette, Belgium, and then with the Benedictines at Downside Abbey, near Bath, England.

In 1851 Vaughan went to Rome, in the Papal States of Italy. He had two years of study at the Collegio Romano, where for a time he shared lodgings with the poet, Aubrey Thomas de Vere. He became a friend and disciple of Henry Edward Manning. Manning, a Catholic convert, became the second Cardinal Archbishop of Westminster following the restoration of the Catholic hierarchy in Great Britain in 1850.