Farquharson won the National Heart Foundation's Award of Merit in 1960, followed by the Pharmaceutical Manufacturers' Association of Canada Health Research Foundation's Medal of Honour in 1964 "for his clinical assessment of antibiotics [and] service as a leading medical educator", becoming one of only 18 people to ever receive this award. He was featured on the cover of Modern Medicine in November 1963. Farquharson was granted honorary degrees by a number of Canadian universities: the University of British Columbia in 1949, the University of Saskatchewan in 1957, Laval University in 1959, Queen's University in 1960, the University of Alberta in 1960, the University of Toronto in 1962, and the University of Montreal in 1965. He was named an honorary member of the Ontario Medical Association. He was also appointed a Knight of the Military and Hospitaller Order of St Lazarus of Jerusalem and an Honorary Fellow of the Royal Society of Medicine in London.
