Vaughan was a survivor of the 1608 sack of Derry during O'Doherty's rebellion. He was made military governor of the town in 1611, repairing the fortifications originally built by Docwra, and was knighted in 1615. He also served as the town's mayor twice, and has been described as "the most outstanding figure in Derry for thirty-five years [...] a permanent element in the government of the town". As governor he was responsible for building many of the town's significant structures, notably Derry city walls and St Columb's Cathedral, completed under his supervision in 1633. Vaughan was responsible for organising the defence of Derry during the 1641 rebellion and early part of the Confederate Wars, but died in 1643 and was succeeded as governor by Robert Stewart.