Thomas was educated at Manila Hall, Clifton, Bristol, before going up to Cambridge University Initially, Thomas was to have gone to Jesus College on a scholarship originally intended for the sons of Anglican Ministers. Since Samuel Thomas was neither an Anglican nor a minister, it would be interesting to know exactly how D. A. Thomas obtained such a scholarship. An attack of Typhoid fever, contracted in Clermont-Ferrand meant that Thomas was unable to take up the scholarship. As it was, Thomas obtained a scholarship to Gonville and Caius College, Cambridge, where he studied mathematics, and would have finished top of his year, if it had not been for his indifferent health. Even so, Thomas was in the University Rowing and Boxing teams. Thomas left Cambridge in 1880, on the death of his father.