He himself confesses in his autobiography that "it was a great error in me to appear in this matter," and his conduct cost him the patronage of the duke of York. In ecclesiastical matters he threw in his lot with Thomas Tillotson and John Tenison, and at the time of the Revolution had written some eighteen polemics against encroachments of the Roman Catholic Church. At the suggestion of Sir William Jones, the attorney-general, he began his History of the Reformation in England, based on original documents. In the necessary research he received some pecuniary help from Robert Boyle, but he was hindered in the preparation of the first part (1679) through being refused access to the Cotton library, possibly by the influence of Lauderdale. For this volume he received the thanks of parliament, and the second and third volumes appeared in 1681 and 1715. In this work he undertook to refute the statements of Nicholas Sanders, whose De Origine et progressu schismatis Anglicani libri tres (Cologne, 1585) was still, in the French translation of Maucroix, the commonly accepted account of the English reformation. Burnet's contradictions of Sanders must not, however, be accepted without independent investigation.
At the time of the Popish Plot in 1678 he displayed some moderation, refusing to believe the charges made against the duke of York, though he chose this time to publish some anti-Roman pamphlets. He tried, at some risk to himself, to save the life of one of the victims, William Staly, and visited William Howard, Viscount Stafford, in the Tower. To the Exclusion Bill he opposed a suggestion of compromise, and it is said that Charles offered him the bishopric of Chichester, "if he would come entirely into his interests." Burnet's reconciliation with the court was short-lived. In January 1680 he addressed to the king a long letter on the subject of his sins; he was known to have received the dangerous confidence of Wilmot, earl of Rochester, in his last illness; and he was even suspected, unjustly, in 1683, of having composed the paper drawn up on the eve of death by William Russell, Lord Russell, whom he attended to the scaffold. On the 5th of November 1684 he preached, at the express wish of his patron Grimston, and against his own desire, the usual anti-Catholic sermon.
He was consequently deprived of his appointments by order of the court, and on the accession of James II. retired to Paris. He had already begun the writing of his memoirs, which were to develop into the History of His Own Time.
Burnet now travelled in Italy, Germany and Switzerland, finally settling in Holland at the Hague, where he won from the princess of Orange a confidence which proved enduring. He rendered a signal service to William by inducing the princess to offer to leave the whole political power in her husband's hands in the event of their succession to the English crown. A prosecution against him for high treason was now set on foot both in England and in Scotland, and he took the precaution of naturalizing himself as a Dutch subject. Lady Margaret Burnet was dying when he left England, and n Holland he married a Dutch heiress of Scottish descent, Mary Scott. He returned to England with William and Mary, and drew up the English text of their declaration. His earlier views on the doctrine of non-resistance had been sensibly modified by what he saw in France after the revocation of the edict of Nantes and by the course of affairs at home, and in 1688 he published an Inquiry into the Measures of Submission to the Supreme Authority in defence of the revolution. He was consecrated to the see of Salisbury on the 31st of March 1689 by a commission of bishops to whom Archbishop Sancroft had delegated his authority, declining personally to perform the office.
In his pastoral letter to his clergy urging them to take the oath of allegiance, Burnet grounded the claim of William and Mary on the right of conquest, a view which gave such offence that the pamphlet was burnt by the common hangman three years later. As bishop he proved an excellent administrator, and gave the closest attention to his pastoral duties. He discouraged plurality of livings, and consequent non-residence, established a school of divinity as Salisbury, and spent much time himself in preparing candidates for confirmation, and in the examination of those who wished to enter the priesthood. Four discourses delivered to the clergy of his diocese were printed in 1694. During Queen Mary's lifetime ecclesiastical patronage passed through her hands, but after her death William III. appointed an ecclesiastical commission on which Burnet was a prominent member, for the disposal of vacant benefices. In 1696 and 1697 he presented memorials to the king suggesting that the first-fruits and tenths raised by the clergy should be devoted to the augmentation of the poorer livings, and though his suggestions were not immediately accepted, they were carried into effect under Queen Anne by the provision known as Queen Anne's Bounty. His second wife died of smallpox in 1698, and in 1700 Burnet married again, his third wife being Elizabeth (1661-1709), widow of Robert Berkeley and daughter of Sir Richard Blake, a rich and charitable woman, known by her Method of Devotion, posthumously published in 1710. In 1699 he was appointed tutor to the royal duke of Gloucester, son of the Princess Anne, an appointment which he accepted somewhat against his will.
His influence at court had declined after the death of Queen Mary; William resented his often officious advice, placed little confidence in his discretion, and soon after his accession is even said to have described him as ein rechter Tartuffe. Burnet made a weighty speech against the bill (1702-1703) directed against the practice of occasional conformity, and was a consistent exponent of Broad Church principles. He devoted five years' labour to his Exposition of the Thirty-nine Articles (1699; ed. J.R. Page, 1837), which was severely criticized by the High Church clergy. But his hopes for a comprehensive scheme which might include nonconformists in the English Church were necessarily destroyed on the accession of Queen Anne. He died on the 17th of March 1715, and was buried in the parish of St James's, Clerkenwell.
Burnet directed in his will that his most important work, the History of His Own Time, should appear six years after his death. It was published (2 vols., 1724-1734) by his sons, Gilbert and Thomas, and then not without omissions. It was attacked in 1724 by John Cockburn in A Specimen of some free and impartial Remarks. Burnet's book naturally aroused much opposition, and there were persistent rumours that the MS. had been unduly tampered with. He has been freely charged with gross misrepresentation, an accusation to which he laid himself open, for instance, in the account of the birth of James, the Old Pretender. His later intimacy with the Marlboroughs made him very lenient where the duke was concerned. The greatest value of his work naturally lies in his account of transactions of which he had personal knowledge, notably in his relation of the church history of Scotland, of the Popish Plot, of the proceedings at the Hague previous to the expedition of William and Mary, and of the personal relations between the joint sovereigns.
Of his children by his second wife, William (d. 1729) became a colonial governor in America; Gilbert (d. 1726) became prebendary of Salisbury in 1715, and chaplain to George I. in 1718; and Sir Thomas (1694-1753), his literary executor and biographer, became in 1741 judge in the court of common pleas.