[2] The son of William Morley Stubbs, a solicitor, and his wife, Mary Ann Henlock, he was born in a house on the High Street in Knaresborough, Yorkshire, and was educated at Ripon Grammar School and Christ Church, Oxford, where he graduated MA in 1848, obtaining a first-class in Literae Humaniores and a third in mathematics.

[3] Stubbs was elected a Fellow of Trinity College, during his time living in Navestock, Essex, from 1850 to 1866, where he served as parish priest for the same period.

He was librarian at Lambeth Palace, and in 1862 was an unsuccessful candidate for the Chichele Professorship of Modern History at Oxford.

He accepted the patronage of the Stubbs Society during his time at Oxford, where he interacted with future doyens of the historical profession.

His opinions were received with marked respect by his brother prelates, and he acted as an assessor to the archbishop in the trial of Edward King, Bishop of Lincoln.

He was able, however, to attend the funeral of Queen Victoria on 2 February 1901, and preached a remarkable sermon[6] before King Edward VII and the German Emperor Wilhelm II on the following day.

While pointing out that history is useful as a mental discipline and a part of a liberal education, he recommended its study chiefly for its own sake.

He was a good palaeographer, and excelled in textual criticism, in examination of authorship, and other such matters, while his vast erudition and retentive memory made him second to none in interpretation and exposition.

Some modern historians have questioned his acceptance of some medieval chronicles, written by monastical scribes whose views would be, to some extent, influenced by the politics of the Catholic Church.

One such criticism was Stubbs's tirade against William Rufus whose character was much-maligned by the chroniclers perhaps due to his opposition to Gregorian reforms during his reign, which led to Archbishop Anselm going into exile.

J. W. Burrow proposed that Stubbs, like John Richard Green and Edward Augustus Freeman, was an historical scholar with little or no experience of public affairs, with views of the present which were romantically historicised and who was drawn to history by what was in a broad sense an antiquarian passion for the past, as well as a patriotic and populist impulse to identify the nation and its institutions as the collective subject of English history, making the new historiography of early medieval times an extension, filling out and democratising, of older Whig notions of continuity.