Wilson was the sixth of seven children and fifth son of Nathaniel Wilson (died 29 May 1702) and Alice Wilson née Browne (died 16 August 1708). He was born at Burton, Cheshire on 20 December 1663. According to Wilson's biographer John Keble, both sides of his family had been Burton residents for many centuries. Much of Wilson's childhood was spent at the parsonage in Winwick where his paternal half-uncle, chaplain Richard Sherlock lived; Sherlock supervised Wilson's training. It was through Sherlock that the earliest connection to the Isle of Man can be made, insofar as he was chaplain to the son of the seventh earl of Derby and Lord of Mann, amongst whose ambitions were to restore order to the church in the Isle of Man after a breakdown in the seventeenth century.