On the death of the Earl of Southampton Bishop Morley ‘took him into his own household,’ and on ‘his dismission from his service with a fair reward’ recommended him in 1666 as chaplain to the Duke of York, afterwards James II, to whose daughter, the Princess Anne, he became tutor.
He was afterwards presented by his friend, Bishop Turner of Ely, to the living of Cottenham, near Cambridge, and promoted by the crown to a canonry at Windsor in 1688.
Fitzwilliam appears to have been a regular attendant at these services, for he admits that ‘he had been a hundred times at prayers in their altered state,’ that is, when the names of King William and Queen Mary were omitted.
Thomas Selwood, who edited the first edition of Lady Russell's letters in 1773, says: ‘All the letters to Dr. Fitzwilliam were by him returned in one packet to her ladyship, with his desire they might be printed for the benefit of the public.’ The correspondence indicates the greatest veneration on the part of Lady Russell for her old instructor, and a pastoral, almost a parental, solicitude on his part for his old pupil.
Anticipating that he would not be able to comply, he adds: 'I beg of your honour three things: first, that you would have the same good opinion of my integrity, and of my zealous addiction to your service, as ever you had; secondly, that you would permit me, in entire trust and confidence, to make over all my worldly goods to you; for I fear some men's hearts may drive affairs so far as to bring all remnants of it into a premunire; thirdly, that I may have some room in your house, if any can be spared, to set up my books in, and have recourse to them if, on refusal, we may be permitted to stay in town.'
He died in 1699, having appointed 'my ever dear friend, and now my truly honoured father,' Dr. Ken, his sole executor under his will, with a life interest in 500 pounds, which he bequeathed to the library of Magdalen College.
The only publication of Fitzwilliam extant is A Sermon preached at Cotenham, near Cambridge, on 9 Sept. 1683, being the day set apart for Public Thanksgiving for deliverance of His Sacred Majesty and Government from the late Treasonable Conspiracy, that is, the Rye House plot, for his supposed complicity in which Lord William Russell lost his life.