In 1819 he entered Bonn University, where he became privatdocent in 1824, extraordinary professor of physiology in 1826, and ordinary professor in 1830. In 1883 he removed to the university of Berlin, where he filled the chair of anatomy and physiology with great distinction until his death. Müller made numerous researches in various departments of physiology, and in particular he extended knowledge as to the mechanism of voice, speech and hearing, and as to the chemical and physical properties of lymph, chyle and blood.
The appearance of his Handbuch der Physiologie des Menschen between 1833 and 1840 (translated into English by Dr William Baly, and published in London in 1842) marked the beginning of a new period in the study of physiology. In it, for the first time, the results of human and comparative anatomy, as well as of chemistry and other departments of physical science, were brought to bear on the investigation of physiological problems.
The most important portion of the work was that dealing with nervous action and the mechanism of the senses. Here he stated the principle, not before recognized, that the kind of sensation following stimulation of a sensory nerve does not depend on the mode of stimulation but upon the nature of the sense-organ. Thus light, pressure, or mechanical stimulation acting on the retina and optic nerve invariably produces luminous impressions. This he termed the law of the specific energy of sense substances. In the later part of his life he chiefly devoted himself to comparative anatomy. Fishes and marine invertebrata were his favorite subjects. Müller numbered such distinguished physiologists as Hermann von Helmholtz, Emil du Bois-Reymond and KFW Ludwig among his pupils.
In addition to his Handbuch der Physiologie, his publications include: