He was demobilised in 1946. On his return to the library, he was promoted to deputy librarian and formed a successful partnership with W. J. Bishop, who succeeded Moorat. The Wellcome Library officially opened in 1949 and with Bishop he encouraged the development of its services and raised its profile via the medical section of the Library Association. Together, they worked on research and bibliography, and in 1953, they also led the organisation of the first International Congress on Medical Librarianship. Its proceedings, edited by Poynter, were published in 1954. When Bishop resigned in 1953, due to frustrations with the Wellcome Historical Medical Museum and its director, Edgar Ashworth Underwood, Poynter took over as librarian and began in this role with the publication of the quarterly "Current Work in the History of Medicine", followed by a catalogue of the library's incunabula. In 1956, Poynter gained a PhD from Westfield College for his work on Gervase Markham. This bibliography was published in 1963. In 1958, Poynter was a key player in founding the Faculty of the History of Medicine and Pharmacy of the Society of Apothecaries, serving first as its secretary and editor of its proceedings, and then as its chairman in 1970. Its success led to the foundation of the BSHM in 1965, when he was one of its founding committee members along with William Copeman, Haldane Philp Tait, K. D. Keele, D. Geraint James, Douglas Guthrie, E. S. Clarke and Charles Newman. Between 1965 and 1967, he was president of the Osler Club of London. He became president of the BSHM in 1972. Poynter was also active in the reorganisation of the Société Internationale d’Histoire de la Médecine, becoming its Secretary-General. He subsequently became the president of the International Academy of the History of Medicine. Following Bishop's death in 1961, Poynter succeeded him as editor of the first exclusive British journal to the history of medicine, "Medical History", a journal he founded and then edited between 1957 and 1973. He was appointed to the editorial board of the "Journal of the History of Medicine and Allied Sciences", with the assistance of his American colleagues. In 1964, Poynter was appointed Director of the Wellcome Institute of the History of Medicine, a position he held until 1973, after which he was succeeded by E. S. Clarke.