Lindsey was born in Middlewich, Cheshire, and was educated at the Leeds Free School and at St John's College, University of Cambridge, where in 1747 he became a fellow. For some time he held a curacy in Spitalfields, London, and from 1754 to 1756 he travelled on the continent of Europe as tutor to the young Duke of Northumberland.
He was then presented to the living of Kirkby-Wiske in Yorkshire, and after exchanging it for that of Piddletown in Dorsetshire, he moved in 1763 to Catterick in Yorkshire. Here about 1764 he founded one of the first Sunday schools in England.
Meanwhile he had begun to entertain anti-Trinitarian views, and to be troubled in conscience about their inconsistency with the Anglican belief; since 1769 the intimate friendship of Joseph Priestley had served to foster his scruples, and in 1771 he united with Francis Blackburne, archdeacon of Cleveland (his father-in-law), John Jebb (1736-1786), Christopher Wyvill (1740-1822) and Edmund Law 1703-1787), bishop of Carlisle, in preparing a petition to Parliament with the prayer that clergymen of the church and graduates of the universities might be relieved from the burden of subscribing to the thirty-nine articles, and "restored to their undoubted rights as Protestants of interpreting Scripture for themselves". Two hundred and fifty signatures were obtained, but in February 1772 the House of Commons declined even to receive the petition by a majority of 217 to 71; the adverse vote was repeated in the following year, and in the end of 1773, seeing no prospect of obtaining within the church the relief which his conscience demanded, Lindsey resigned as vicar.
In April 1774 he began to conduct Unitarian services in a room in Essex Street, the Strand, London, where first a church (Essex Street Chapel), and afterwards the Unitarian offices (first the British and Foreign Unitarian Association and then the General Assembly of Unitarian and Free Christian Churches), were established. Here he remained till 1793 when he resigned his charge in favour of John Disney, who like himself had left the established church and had become his colleague.
In 1800 he received a considerable bequest from Elizabeth Rayner, a wealthy member of his congregation, and as a result his final years were spent in comfort. He died at home in Essex Street on 3 November 1808, and was buried in Bunhill Fields burial ground. By Elizabeth Rayner's request, her remains were placed in the same grave. Lindsey was succeeded as minister at Essex Street from 1805 by Thomas Belsham, who wrote Lindsey's biography (published in 1812), and who, following his own death in 1829, was also buried in the same grave.
Lindsey's chief work was An Historical View of the State of the Unitarian Doctrine and Worship from the Reformation to our own Times (1783).
His other publications included:
- Apology on Resigning the Vicarage of Catterick (1774)
- Sequel to the Apology (1776)
- The Book of Common Prayer, reformed according to the plan of the late Dr Samuel Clarke (1774)
- Dissertations on the Preface to St John's Gospel and on praying to Jesus Christ (1779)
- Vindiciae Priestleianae (1788)
- Conversations upon Christian Idolatry (1792)
- Conversations on the Divine Government, shewing that everything is from God, and for good, to all (1802).
Two volumes of sermons, with appropriate prayers annexed, were published posthumously in 1810.
Thomas Belsham's Memoirs of the Late Reverend Theophilus Lindsey, M.A., including a brief analysis of his works; together with anecdotes and letters of eminent persons, his friends and correspondents; also a general view of the progress of the Unitarian doctrine in England and America appeared in 1812.
- "Lindsey, Theophilus (LNDY741T)". A Cambridge Alumni Database. University of Cambridge.