The son of a well known lawyer, John Cuningham was born in Christchurch, New Zealand and educated at St Andrew's College, and subsequently at Otago Medical School, Dunedin. He qualified in 1940, and then spent two years as house physician at New Plymouth Hospital. His postgraduate medical education was interrupted by war service. He entered the Royal New Zealand Air Force and, as a flight lieutenant, served in New Zealand, New Caledonia, New Hebrides and the Solomon Islands.

After demobilisation in 1946, John Cuningham spent six months as medical registrar at Waikato Hospital before going to Britain for further medical training. He was appointed house physician at Hammersmith Hospital, became a member of the Royal College of Physicians in 1947, and then spent a year at Johns Hopkins Hospital, Baltimore. He returned to New Zealand having accepted a position as senior medical registrar at Christchurch Hospital.

He held the Christchurch post until 1953, when he was appointed to the staff as a part-time general physician. He became a member of The Royal Australasian College of Physicians and was elected to Fellowship in 1959. In 1969, he became a Fellow of the London College. In the mid-1960s, a Pfizer Fellowship enabled him to return to Johns Hopkins for studies in neurology. Although trained as a general physician, his real love was for neurology and this special interest was to continue for the rest of his life. A few years later he spent a further term in Baltimore to observe the growing use of electroencephalography. As a skilful and well informed clinician, Cuningham developed a successful consulting practice in Christchurch where his shrewd judgement and sharp wit were very much in demand. From 1972, he restricted his hospital and private practice to neurology. He made a considerable contribution to the establishment of a neurology department and became an active member of the newly formed Neurology Association of New Zealand.

Cuningham's ward rounds were popular with both students and housemen. He became well known for his scathing comments on what he considered to be unnecessary and wasteful use of laboratory tests and drug administration. His comments would end with a homily on the importance of clinical judgement and common sense. Cuningham was chairman of the Christchurch Hospitals' Medical Staff Association from 1974 to 1976. He was a regular attender at College meetings at which he made many scientific contributions – usually an account of some unusual phenomenon or rare syndrome based on his own clinical observation, and presented in a characteristic precise way. He was a shy man who did not seek prominence in the Colleges of which he was a Fellow but he was always ready to assist with the organisation of College meetings.

For the last 10 years until the onset of his final illness, 'Jake', as he was called by those who knew him, was the sole neurology consultant in Christchurch. During these years he was consultant to the spinal injuries unit, to the regional psychiatric hospital and to the Christchurch Women's Hospital. He was also consultant to the Accident Compensation Corporation.

Jake did not have much time for sport, although when a school boy he had excelled at running and rugby. During his adult life he still enjoyed tramping and hill climbing. This was a sport that he could share with his family. John Cuningham's fine brain was eventually destroyed by Alzheimer's disease and he died leaving behind him his devoted wife Yatela, and two children, Andrew and Jessica.