He was the grandson of Colonel Baker of Crook, Durham, who won fame in the English Civil War by his defence of Newcastle upon Tyne against the Scots.
Thomas was educated at the free school at Durham, and went on to St John's College, Cambridge, where he later obtained a fellowship.
[1] Lord Crew, bishop of Durham, collated him to the rectory of Long Newton in his diocese in 1687, and intended to give him that of Sedgefield with a prebend had not Baker incurred his displeasure by refusing to read James II's Declaration of Indulgence.
Baker, though he had opposed James, refused to take the oaths to William; he resigned Long Newton on 1 August 1690, and retired to St John's, in which he was protected till 20 January 1716/1717, when he and twenty-one others were deprived of their fellowships.
The only works he published were Reflections on Learning, showing the Insufficiency thereof in its several particulars, in order to evince the usefulness and necessity of Revelation (London, 1709–1710) and the preface to Bishop Fisher's Funeral Sermon for Margaret, Countess of Richmond and Derby (1708)—both without his name.