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- Life and Opinions of John de Wycliffe, D.D., illustrated principally from his unpublished Manuscripts (1828)
- Memorials of the Stuart Dynasty (1831)
- The Christian Warfare (1832)
- On the Study of General History (1834)
- Causes of the Corruption of Christianity (1834)
- Thoughts on the … State of Religious Parties in England (1838)
- Protectorate of Oliver Cromwell (1838), in 2 vols.
- The History of England under the House of Stuart … 1603–88 (1840)
- Congregationalism … in relation to … Modern Society (1842)
- The Modern Persecutor Delineated (1842)
- The Modern Pulpit (1842)
- The Age of Great Cities (1843)
- Protestant Nonconformity (1843)
- Tracts and Treatises of John de Wycliffe … with … Memoir (1845)
- Popular Education in England (1846)
- Essays on History, Philosophy, and Theology (1849), in 2 vols.
- The Age of Christianity (1849)
- John de Wycliffe, D.D.: a Monograph (1853)
- The Credulities of Scepticism (1856)
- Revolutions in English History (1859–63), in 3 vols.
- I'll tell you: an Answer to “How did they get there?" (1862)
- English Nonconformity (1862)
- Ritualism in the English Church (1866)
- The Way to Rest (1866)
- The Church and State Question 
- The Daily Prayer Book 
Works about Vaughan
- "Vaughan, Robert (1795-1868)," in Dictionary of National Biography, 1885-1900, London: Smith, Elder, & Co. (1885–1900) in 63 vols.
- "Vaughan, Robert," in A Short Biographical Dictionary of English Literature, by John William Cousin, London: J. M. Dent & Sons (1910)
Some or all works by this author were published before January 1, 1928, and are in the public domain worldwide because the author died at least 100 years ago. Translations or editions published later may be copyrighted. Posthumous works may be copyrighted based on how long they have been published in certain countries and areas.