Frederic Watkyn-Thomas was born on 10 April 1887, son of William Watkyn-Thomas of Papcastle, Cumberland (c 1853-1925), civil engineer, and his wife Katharine Mary, née Waite (c 1858-1927). He was educated at Tonbridge School and was admitted to Trinity College Cambridge in 1906, where he was an exhibitioner and Bean W. Levy student, obtaining his Bachelor of Medicine in 1914. He completed his clinical studies at St Bartholomew's Hospital, London and was awarded the Brackenbury and Holden scholarships. Qualifying as a Doctor of Medicine in 1914, he entered the Royal Army Medical Corps immediately, serving until 1920 when he was demobilised with the rank of Major.
He was admitted as a Fellow of the Royal College of Surgeons (RCS) of England in 1921, and appointed to the consultant staff of the Central London Throat, Nose and Ear Hospital (which later became the Royal National Throat, Nose and Ear Hospital). In 1933 he joined the staff of the Royal Ear Hospital, part of University College Hospital. For many years he was a civilian consultant to the Royal Navy and became a member of the Royal Navy Personnel Research Committee and the Flying Research Committee. As well as serving as President of the Section of Otology of the Royal Society of Medicine, he was on the council of the British Association of Otorhinolaryngologists, Abstracts Editor for the Journal of Laryngology and a regular contributor to the Medical Annual until 1954. In 1953 he edited a textbook on Diseases of the Throat, Nose and Ear and wrote the entire section on the ear himself.
He married Ada Margaret Catherine Macgregor Clayton (1889-1985), daughter of Walter Norton Clayton and Annie Macpherson Macgregor and known as Diana to her family and friends, in January 1928.