Vaughan, Sir John (d. 1643), servitor, was born in Wales. He arrived in Ireland in early 1599 as a lieutenant in reinforcements sent from the Low Countries. In May 1600 he landed in Lough Foyle as part of an expedition to Ulster led by Sir Henry Docwra (qv). He became a captain in June and was well regarded by his commander. In late 1600 he played an important but obscure role in securing the submission of the O’Dohertys. He was in England from March to July 1601, gathering reinforcements for Lough Foyle. After the end of the Nine Years War, he remained in Derry, where he commanded a company and received a government pension. By 1608 he also held the fort of Dunalong and the surrounding land. In 1608 Sir Cahir O'Doherty (qv) seized and burnt Derry, killing the governor, George Paulet (qv). After the suppression of this revolt Vaughan was made governor of Derry. His local knowledge and training as a military engineer made him ideally suited for overseeing the laborious task of rebuilding the settlement. Thereafter he was the dominant figure in the development of Derry (after 1613, Londonderry), supervising the construction of the city's walls (1614–18) and cathedral (1628–33).
Under the plantation of Ulster in 1611 he received 2,000 acres in the barony of Kilmacrennan, Donegal, 1,000 acres of which he later sold. In late 1612 he purchased 1,000 acres at Lifford, Donegal. He also leased land in Inishowen. As well as serving as governor of Derry until his death, he was sheriff of Donegal (1610), alderman of Londonderry (1613–43), mayor of Londonderry (May 1617 to February 1618, and April 1627 to July 1630), head of the Londonderry staple (1621) and MP for Donegal county (1613–15 and 1634–5). His influence in west Ulster was recognised by the central administration, which knighted him 2 February 1617 and made him a member of the Irish privy council in December 1623. He sat on a number of commissions to inquire into abuses in the plantations in Londonderry, and collected subsidies for the army in Donegal and Londonderry in 1627.
From 1613 the city of London's plantation in Londonderry seriously weakened his local hegemony. In 1614 the city vetoed his appointment as mayor of Londonderry. He later came to an accommodation with the Londoners and in 1628 he was criticised for overlooking abuses committed by the city in its plantation. After the outbreak of the 1641 rebellion, he held Londonderry for the government but due to his age played only a minor role in the fighting. He died shortly before April 1643 in Londonderry.