In 1945 he moved to become head physicist at the Royal Victoria Infirmary (RVI) in Newcastle-Upon-Tyne. The hospital at that time had Marconi deep therapy X-Ray machines installed, with which Farmer was closely familiar from his time working at Marconi, and as a result the hospital was able to keep these machines in clinical use for many years. Farmer's team brought together experts in health physics, radio-isotopes, ultrasonics, instrumentation and physiological measurement. Specific innovations included the world's first gantry-mounted linear particle accelerator for cancer treatment, installed in 1963, and numerous clinical uses of the radioisotope tracer technique, developed using radio-isotopes from the nuclear reactors at Amersham and Harwell, which became available to researchers after World War II. When the new department opened, Farmer was appointed first Professor of Medical Physics at Newcastle University in 1966. While at the RVI, Farmer and his team turned the facility into a renowned centre for research into medical applications of radio-isotope technology, providing services in these areas to the entire region of Northern England, which had previously had none. At the time of Frank Farmer's retirement in 1978, the department had branches in Teesside and Cumbria, as well as the three hospitals in Newcastle, and employed 70 scientific and technical staff.