Macintyre was born in High Street, Glasgow in a family of a tailor. His mother was related to the missionary and explorer David Livingstone. Macintyre originally trained as an electrical engineer and worked as an apprentice electrician before enrolling to the University of Glasgow in 1878. There he changed his field for medicine and graduated in 1882 with the Bachelor of Medicine degree. He then worked as a naval surgeon in London, Paris and Vienna, and returned to Glasgow to assume a position of a Surgeon for Diseases of the Throat at Anderson's College Dispensary. He later established a private practice specialising in the treatment of singers and actors.
Macintyre is mostly known for applying his electrical engineering knowledge to medicine. In 1885 he became Consulting Medical Electrician at Glasgow Royal Infirmary where he established a "department for the application of medical electricity" in 1887. Soon after X-rays were discovered by Wilhelm Röntgen, Macintyre set up an X-ray machine in his laboratory and reproduced the Röntgen's experiment of producing an image of the bones of own hand. He went further and recorded an X-ray movie of the moving legs of a frog, and presented the results in a report "On Roentgen X-Rays, or the new photography" to the Philosophical Society of Glasgow in 1896. In the same year, he set up the world's first radiology department at the Glasgow Royal Infirmary, where X-ray photographs were used in the diagnosis and treatment of patients. There, Macintyre produced the first images of renal stones and various inner body parts. For his groundbreaking work, he received many awards and honours. He served as President of the British Laryngological, Rhinological, and Otological Association in 1893 and 1900, co-editor of the British Journal of Laryngology, Rhinology, and Otology, President of the Rontgen Society, President and of the West of Scotland Branch of the British Medical Association, Corresponding Fellow of the American and French Laryngological Associations, Fellow of the Royal Society of Edinburgh and of the Royal Microscopical Society, among other posts.