Thomas was the son of John Stackhouse (d. 1734), ultimately Rector of Boldon, co. Durham, and was born in Witton-le-Wear in that county, where his father was then curate, in 1677. On 3rd April 1694, he was entered at St. John's College, Cambridge, but the designation of 'M.A.' which appears on the title pages of some of his works does not seem to represent a degree derived from an English university. It was possibly obtained, as the tradition in his family runs, during his residence abroad. From 1701 to 1704, he was headmaster of Hexham Grammar School, and on 28th December 1704, he was ordained a priest in London. He then became Curate of Shepperton in Middlesex and, from 1713, was minister of the English Church at Amsterdam. In I731, he was Curate of Finchley.

For some time, Stackhouse lived in poverty and, in 1722, under the designation of 'A Clergyman of the Church of England,' addressed a printed letter to Bishop John Robinson (1650-1723) exposing the 'miseries and great hardships of the inferior clergy in and about London'. It was re-issued and the later editions bore his name on the title page. In 1732, while engaged on his great 'History of the Bible,' he issued a pamphlet (now very scarce) called 'Bookbinder, Bookprinter and Bookseller confuted; or Author's Vindication of himself,' which related his troubles with two booksellers. From a condition of extreme distress, he was rescued by his appointment, in the Summer of 1733, to the vicarage of Beenham (sometimes called, incorrectly, Beenham Valence) in Berkshire. In 1737, when he had a house in Theobald's Court, London, he acknowledged that he owed to Edmund Gibson, Bishop of London, "the present comfortable leisure for study and the generous encouragement" to his labours. In 1741, he was living in Chelsea and, no doubt, was often non-resident and working for the booksellers. He died at Beenham on 11th October 1752 and was buried in the parish church, a monument being placed there to his memory. By his first wife, who died in 1709, he had two sons, and by his second wife, Elizabeth Reynell, two sons and one daughter.

The great work of Stackhouse was his 'New History of the Holy Bible from the Beginning of the World to the Establishment of Christianity,' which tradition says, being rather too fond of a drink, he wrote in the 'Three Kings - Jack's Booth' public house in Sulhamstead, just across the Kennet Valley from Beenham. He brought it out in numbers and then published in two folio volumes in 1737, with a dedication to his patron, Bishop Gibson. The second edition came out in two folio volumes in 1742-4, and it was often reprinted, with additional notes, by other divines. The work was illustrated with many views, including the ark inside and outside, and the Tower of Babel. The plate of the 'Witch of Endor' was the bugbear of the childhood of Charles Lamb, and the quaint representation of the 'elephant and camel' peeping out from the ark, Lamb never forgot. The illustrations were altered in the later editions. This work is said by Orme to be wanting in originality and profundity, but it states infidel objections with some power. Trusler compiled from it in 1797 'A Compendium of Sacred History.'

Besides sermons, Stackhouse published: 1. 'Memoirs of the Life and Conduct of Bishop Atterbury, by Philalethes' (1723); 2. An abridgment of Burnet's 'History of his own Times' (1724); 3. 'New Translation of Drelincourt's Consolations against Death' (1725); 4. 'A Complete Body of Divinity in Five Parts, from the best Ancient and Modern Writers' (1729); 5. 'A fair State of the Controversy between Mr. Woolston and his Adversaries' (1730); 6. 'Defence of the Christian Religion, with the whole state of the Controversy between Mr. Woolston and his Assailants' (173l); 7. 'Reflections on Languages in General, and on the Advantages, Defects, and Manner of improving the English Tongue in particular' (1731); 8. 'A New and Practical Exposi-tion of the Apostles' Creed' (1747); 9. 'Varia doctrinae emolumenta, et varia Studiorum incommoda . . . versa hexametro exarata' (1752); 10. 'Life of Our Lord and Saviour, with the Lives of the Apostles and Evangelists' (1754).

Stackhouse added to the third volume of the works of Archbishop Dawes, a supplemen, of a regular course of devotions. He is sometimes credited with the authorship of 'The Art of Shorthand on a New Plan' by 'Thomas Stackhouse, A..M.' [1760?]. The topographical account of Bridgnorth communicated (about 1740) to the 'Philosophical Transactions', and sometimes attributed to him, was written by the Rev. Hugh Stackhouse, minister of St. Leonard and St. Mary Magdalene in that town and Rector of Oldbury, who died in April 1743.