[1] In 1855, Fowler was elected a Fellow of Lincoln College, Oxford and was forthwith appointed tutor.

[1] Fowler was a junior contemporary of men like Benjamin Jowett, Arthur Stanley, Goldwin Smith, Mark Pattison (whom he might have succeeded as Rector of Lincoln), John Matthias Wilson (whom he succeeded as President of Corpus), and Dr Henry Liddell, sometime Dean of Christ Church.

His works included two volumes on Deductive and Inductive Logic respectively, which have passed through many editions, and are, in the main, a reproduction for Oxford use of the logical system of John Stuart Mill; an elaborate edition of Francis Bacon's Novum Organon, with introduction and notes; an edition of Locke's Conduct of the Understanding; monographs on John Locke, Bacon and Shaftesbury and Hutcheson; Progressive Morality, an Essay in Ethics; and The Principles of Morality, an important and original work, which incorporates as much of the thought of J. M. Wilson as Wilson ever managed to put on paper.

[2] In 1881, Fowler was elected,[3] rather unexpectedly, to succeed Professor John Matthias Wilson as President of Corpus Christi College, Oxford.

He wrote its history in a well-researched volume displaying much patient research which was published by the Oxford Historical Society.