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son of Thomas Watts Allen, was born at Geelong, Victoria, on 13 June 1854. He was educated at Flinders School, Geelong, and Melbourne Church of England Grammar School. At the matriculation examination in 1870 he won the exhibitions in classics, mathematics, and English and French. At the university of Melbourne he secured first-class honours in every year of his course, and graduated M.B. in 1876, M.D. in 1878, and B.S. in 1879. In 1876 he was appointed demonstrator in anatomy, in 1882 he became lecturer in anatomy and pathology, and from the beginning of 1883 was professor in these subjects. He was also pathologist at the Melbourne Hospital. He had been editor of the Australian Medical Journal from 1879, but pressure of work now obliged him to give up this office. As a result of strong representations the government of Victoria had provided the funds for a building for the medical school, and Allen was asked to collaborate with the government architects in preparing the plans. He also succeeded in having the collection of pathological specimens at the Melbourne Hospital transferred to the university, and thus began the pathological museum to which he was henceforth to give much time. It eventually became a great collection that was invaluable in connexion with the teaching of the subject. In the same year he was appointed to the central board of health, for which he drew up a set of by-laws for the use of local health authorities, and he did valuable work in connexion with an inquiry into tuberculosis in cattle, and also in connexion with freezing chambers for the frozen meat trade, then in its infancy. In 1886 Allen became dean of the faculty of medicine and succeeded in bringing in an amended curriculum for the medical course. In 1888 he was made president of the royal commission appointed to inquire into the sanitary state of Melbourne; typhoid fever was then common and the commission's report included the recommendation that a water-borne sewerage system should be adopted. This however was not commenced for some years. Allen was appointed president of the intercolonial rabbit commission in 1889; he was only 35, but his reputation was already spreading beyond Victoria. In the same year he was general secretary of the intercolonial medical congress, held at Melbourne. His next important work was the obtaining of recognition of Melbourne medical degrees in Great Britain. The university petitioned the privy council and Allen was sent to England in 1890 to support the petition. He succeeded in satisfying the general medical council that the Melbourne curriculum was among the best in existence and the recognition was granted.

Allen was elected to the university council in 1898, the first professor to be a member of that body. He was a most valuable member, constant in attendance and interested in the welfare of every department. Dr C. J. Martin who was subsequently to have a distinguished career in Europe had been appointed lecturer in physiology in 1894 and Allen encouraged him in every way, eventually recommending that he should be given the title of acting-professor. Martin resigned in 1903 to become director of the Lister Institute of Preventive Medicine, London. Dr W. A. Osborne was appointed to take his place in 1904 as professor of physiology and in 1906 Dr R. J. A. Berry was appointed to the chair of anatomy, Allen taking the title of professor of pathology. A well-equipped laboratory of bacteriology had been established, and Allen could now feel that he had a medical school in which he could take some pride. But though apparently wrapped up in his department, he was able to spare time to do valuable work outside it. There were two medical societies in Melbourne, the Medical Society of Victoria, and the Victorian branch of the British Medical Association, and in 1906 Allen succeeded in healing the breach between them. In the same year there was a strong difference of opinion as to whether the proposed Institute of Tropical Medicine should be established at Sydney or Townsville. A committee was formed with Allen as chairman. Anderson Stuart (q.v.), a man of much personality, was in favour of Sydney, but Allen succeeded in persuading him to withdraw his opposition. Allen was elected president of the Australasian medical congress held in Melbourne in 1908, an honour he valued very much. In 1912 he visited Europe and represented his university at the congress of universities of the empire and at the bicentenary of the medical school of Trinity College, Dublin. He was everywhere recognized as a pathologist of the highest standing. In 1914 came the jubilee of the medical school at Melbourne and the opportunity was taken of presenting an excellent portrait of Allen by E. Phillips Fox (q.v.) to the university, the cost of which was subscribed by its medical graduates. A report of the various proceedings was published in 1914, University of Melbourne Medical School Jubilee. To this Allen contributed the opening chapter "A History of the Medical School". With the coming of the war he quickly realized that his students would do more valuable work by remaining and completing their courses than by enlisting as combatants. He himself worked at great pressure and possibly laid the seeds of his later break-down. In 1919 he published Pathology. Notes of Lectures and Demonstrations, a volume of nearly 500 pages. He drafted a new medical curriculum in 1921, which was adopted, but fell ill in 1923, and though he temporarily recovered, a serious cerebral haemorrhage so incapacitated him that he was obliged to give up his chair. He died at Melbourne on 28 March 1926. He married in 1891 Ada, daughter of Henry Mason, who survived him with three daughters, one of whom, Mary Allen, became well-known in the United States as a painter and lecturer on art. Allen was given the honorary degree of LL.D. by the university of Edinburgh in 1912, and was knighted in 1914. An elder brother, George Thomas Allen, C.M.G., held a distinguished position in the Commonwealth public service.

Allen lived for his work but was also interested in literature and in art. He was not without vanity, lacked humour, and made comparatively few close friends; but there was an immense earnestness in his character, and a constant striving after the best, which commanded respect. He had untiring energy, great powers of organization, and a remarkable memory. His post-mortem demonstrations were models of their kind; he was ambidextrous and showed absolute control of the materials, complete knowledge, and had a burning desire that the students should understand everything that could be learned from the particular subject. His lectures were concise and orderly, consistently keeping a very high level of instruction, and his department was run with tact and efficiency. When he first became a lecturer he shouldered everything that came his way and gradually became the guiding force in the department. Halford (q.v.) had laid the foundations, and considering his manifold duties had done remarkable work, but it fell to Allen to develop a really great medical school at Melbourne. Another of his monuments is the Walter and Eliza Hall Institute which, the memorial plate to Allen at the Royal Melbourne Hospital states, owed its origin to his inspiration.