He was born the eldest son of John Thompson [sic] of Kelswick House, near Whitehaven, Cumberland, and educated at Shrewsbury School and at The Queen's College, Oxford, of which he became a scholar.

In 1847 he was made tutor of his college, and in 1853 he delivered the Bampton lectures, his subject being The Atoning Work of Christ viewed in Relation to some Ancient Theories.

In the same year he edited Aids to Faith, a volume written in opposition to Essays and Reviews, the progressive sentiments of which had stirred up controversy in the Church of England.

In this position his moderate orthodoxy led him to join Archbishop Archibald Campbell Tait in supporting the Public Worship Regulation Act, and, as president of the northern convocation, he came frequently into sharp collision with the lower house of that body.

But if he thus incurred the hostility of the High Church party among the clergy, he was admired by the laity for his strong sense, his clear and forcible reasoning, and his wide knowledge, and he remained to the last a power in the north of England.