Wilson was tutored at The King's School, Chester and entered Trinity College, Dublin as a sizar on 29 May 1682. His tutor was John Barton, afterwards dean of Ardagh. Jonathan Swift entered in the previous month, and other contemporaries included Peter Browne and Edward Chandler. He was elected scholar on 4 June 1683. In February 1686 he graduated with a B.A.. The influence of Archdeacon Michael Hewetson (died 1709), a prebendary of St Patrick's Cathedral, turned his thoughts from medicine to the church. He was ordained deacon before attaining the canonical age by William Moreton, bishop of Kildare on 29 June 1686 in the cathedral church of Kildare on the day of its consecration.