Through the patronage of the Earl of Leicester, he was collated to the Deanery of Durham, but in 1579 action was started to deprive him of all holy orders on account of his Presbyterian ordination.
Born at Chester about 1524, he was son of William Whittingham, by his wife, a daughter of Haughton of Hoghton Tower, Lancashire.
Whittingham had adopted radical Puritan views, but the accession of Queen Mary, the return of Anglo-Italian ecclesiastical policies of De Haeretico Comburendo in the form of Cardinal Pole's repatriation to England, and the vulnerabilities and liabilities associated with burnings-to-come (e.g. William Tyndale, 1536), anticipated persecutions, interfered with hopes of usefulness in ministerial labours.
Late in August, however, he made intercession, which was ultimately successful, for the release of Peter Martyr; but after a few weeks he himself left England with difficulty by way of Dover to France.
He procured a letter from John Calvin, dated 18 January 1555, which prevailed; but the compromise adopted was disturbed by the arrival and public disruptions of Richard Cox, an uncompromising champion of the 1552 Book of Common Prayer.
In the party with Cox was John Jewel, the famed later bishop of Salisbury, who resolutely opposed Whittingham and Knox in their program.
There exists a nearly eye-witness narrative of the conflict, published in 1575, entitled 'A Brieff Discours off the Troubles begonne at Franckford in Germany, anno Domini 1554.
Abowte the Booke off Common Prayer and Ceremonies, and continued by the Englishe men theyre to thende off Q. Maries Raigne,' 1575.
As well, he was the Latin translator of the martyr Nicholas Ridley's 'Brief Declaration of the Lord's Supper' (Oxford, 1555); regarding his translation, a recent editor of the Declaration said this:"... the Latin Version, to a reader who has learnt to love Ridley's noble combination of courage and decision with fairness of thought and restraint of expression, is a painful study.
He won general praise; but William Cecil complained of his neglect of conformity to the English Book of Common Prayer.
Owing to the support of Warwick and Robert Dudley, 1st Earl of Leicester, another Puritan sympathizer, Whittingham was collated on 19 July 1563 to the deanery of Durham.
Before the outbreak of the Rising of the North in 1569 he unsuccessfully urged James Pilkington, the bishop of Durham, to put the city in a state of defence, but he was more successful at Newcastle, which resisted the rebels.
In 1564, Whittingham wrote a long letter to Leicester protesting against the 'old popish apparel' and the historic associations with Massing-vestments and theology.
Whittingham eventually yielded, taking Calvin's moderating advice not to leave the ministry for external and minor matters of order.
In 1577, however, he incurred the enmity of Edwin Sandys, the new archbishop of York, by resisting his claim to visit Durham Cathedral.
Archbishop Sandys further added that Whittingham had not even been validly ordained even according to Genevan standards, but had been elected preacher without the imposition of hands.
However Archbishop Richard Bancroft, in 'Dangerous Positions', referred to him as 'afterward unworthily Dean of Durham', and ranks him with Goodman, Gilby, and other Puritans.