Vaughan was the eldest son of Howel Vaughan of Glan-y-Llyn, Merioneth and his wife Elizabeth Jones, daughter of Humphrey Jones of Ddol, Flintshire. He inherited from his wife's uncle Edward Vaughan MP, the estates of Llwydiarth and Llangedwyn, Denbighshire in 1661 and succeeded his father in 1669. He married Mary Purcell, daughter of John Purcell, MP of Nantcribba in 1672.[1]
Vaughan died in December 1718. He had two daughters and one son, who predeceased him. His property went to his son-in-law, Watkin Williams Wynn who married his daughter Ann.[3]