Duncan stayed in Hungary for two years, until the Disruption of 1843 led to an invitation to fill the chair of Hebrew and Oriental Languages at New College, Edinburgh.

His tombstone refers to him as "an eminent scholar and metaphysician, a profound theologian, a man of tender piety and of a lowly loving spirit."

[5] Sinclair describes him as "remarkably absent-minded, in regard to the common things of life," but "intensely exercised about the higher and eternal realities.

Referring to the linguistic powers of Alexander Black and his colleague, John Duncan, Thomas Guthrie used to say that ‘they could speak their way to the wall of China;’ yet no corresponding products of their learning were given to the public.

"[8] William Garden Blaikie suggested that "his profound originality, his intellectual honesty, his deep piety, and childlike simplicity, humility, and affectionateness, commanded the respect of every student.

Some considered that the Church would have been better served if he had been permitted to abandon formal lectures in order to conduct walks twice a week with his students in Edinburgh's Princes Street Gardens.

The primary source for many of Duncan's striking aphorisms is the volume compiled by another of his students, William Knight, Colloquia Peripatetica: Deep Sea Soundings (Edinburgh: David Douglas, 1889).