During a 28-year practice in Leeds, Allbutt made valuable clinical studies, primarily of arterial and nervous disorders. In 1866 he introduced the modern clinical thermometer, a welcome alternative to the foot-long instrument that required 20 minutes to register a patient's temperature. In 1871 he published a monograph outlining use of the ophthalmoscope (used to inspect the interior of the eye) as a diagnostic instrument. In 1892 Allbutt became regius professor of physic at the University of Cambridge, where he spent the rest of his career. Continuing his previous work, he postulated that the painful heart condition angina pectoris originates in the aorta (1894).

Allbutt was also a noted medical historian. Two of his most important publications were Diseases of the Arteries, Including Angina Pectoris (1915) and Greek Medicine in Rome (1921). He also edited A System of Medicine, 8 vol. (1896–99). He was knighted in 1907.