He was the son of James Whitaker, innkeeper, and was born in Manchester on 27 April 1735. In 1771, he published the first volume of The History of Manchester; and the second volume in 1775. A copy of Whitaker's manuscript of the continuation to the fifteenth century is in Chetham's Library, Manchester.
Whitaker's views on early British society were idiosyncratic: in his History of Manchester, (1771–75) he argued that the ancient Britons had already established a feudal system, and under the Romans had been entirely converted to Christianity (his erudition was recognised as remarkable but the theories were mostly illfounded). The Life of St Neot, published posthumously in 1809, was similarly intended to challenge traditional orthodoxies in the form of the extant saint's lives.
He took his degrees at Oxford: B.A. 1755; M.A. 1759; and B.D. 1767: he was elected a Fellow of the Society of Antiquaries of London in 1771. After taking his degrees and holding two curacies he became Rector of Ruan Lanihorne in Cornwall in 1777 or 1778. He also published a number of sermons, poems, and articles for Richard Polwhele's History of Cornwall. He was a prolific reviewer for the English Review, British Critic, and Anti-Jacobin Review, finding this an important means of supplementing his income and paying for the books necessary for his studies. In addition to his published works he had planned or contemplated a number of other projects: a parochial history of Cornwall, a military history of the Romans in Britain, a history of Oxford, one of London, notes on Shakespeare, and illustrations to the Bible. He was a man of fiery temperament and extreme views, and a fervent belief in all the tenets of ‘orthodox’ Christianity. He was able to inspire considerable friendship and loyalty from those who knew him best. His close friend Richard Polwhele described him as being of a tall, muscular frame, dark featured, and with light greenish eyes. He reputedly had a squint and wore false teeth made of ebony. He died at his rectory on 30 October 1808 and was buried in Ruan Lanihorne in Cornwall; his widow Jane (née Tregenna), who had long suffered ill health, lived on until 30 December 1828.
He studied the decline of the Cornish language and concluded in his work The Ancient Cathedral of Cornwall
- The English Liturgy, was not desired by the Cornish, but forced upon them by the tyranny of England, at a time when the English language was yet unknown in Cornwall. This act of tyranny was at once gross barbarity to the Cornish people, and a death blow to the Cornish language.