He was born on 6 April 1645 the son of N. N. Wilkie. His uncle Rev Thomas Wilkie (1638-1717) was the minister of Tolbooth Parish in Edinburgh (housed in St Giles Cathedral), the parish which was the forerunner of
Canongate Kirk. He studied at
Edinburgh University and graduated MA in 1662. In January 1672 he translated from Galashiels Parish Church to
North Leith Parish Church in the harbour district of
Edinburgh. In 1687 he moved to Tolbooth Parish in Edinburgh town centre. In 1678, Hector Allan, a Quaker in Leith was found guilty of "abusing and railing" (i.e. verbally insulting) Thomas Wilkie and was rather harshly sent to the prison on the
Bass Rock for this. He was later instead placed in the Leith Tolbooth (prison) until he repented. He was the first minister to preach in the new Canongate Kirk following its construction (begun in 1688). He was placed as minister of the Canongate congregation in May 1689 but spent over two years preaching from their temporary home at
Lady Yester's Church near the Edinburgh High School. He is buried in
Canongate Kirkyard against the east wall of the church. His will bequeathed 400 books to Edinburgh University's Divinity Hall. ==Family==