Johannes Müller was born in Koblenz, Germany on 14 July 1801 and received his medical education at the University of Bonn beginning in 1819 and receiving his doctorate in 1822 following the submission of a thesis entitled De Phoronomia Animalium. He then went to Berlin to sit the state examination for his physician's license before establishing himself in private practice in Bonn. Here he lectured on anatomy, pathology, and diseases of the eye and ear and also Privatdocent. He became associate professor in 1826 and full professor in 1830 before being appointed to the chair of anatomy and physiology in Berlin in 1833, but the political disturbances of 1848 forced him to resign this post.
Müller dedicated much of his time to the study of comparative anatomy and in his later work placed a particular focus on the comparative anatomy and morphology of marine animals. He made a number of discoveries in the field of physiology of the senses in addition to embryology, pathology, and neurophysiology, in particular the chondrin and parameonephric duct, which bears his name and is known as the "Müllerian duct". His main publication in the field was entitled Handbuch der Physiologie des Menschen (2 vols, 1834-40) and his other works include Über die phantastischen Gesichtserscheinungen (1826) and Zur vergleichenden Physiologie des Gesichtssines der Menschen und der Thiere (1826). He also edited the journal Archiv für Physiologie und Anatomie from 1834 onwards.
Müller was found dead in his room in Berlin on 28 April 1858 with some suspecting suicide.