Born at Bern in Switzerland, Haller studied under Hermann Boerhaave at Leiden, gaining his MD in 1727. He was later appointed professor of anatomy, botany, and medicine (1736–53) at the newly established University of Göttingen. He then retired to Bern to spend more time on his research and writing.

Between 1757 and 1766 Haller published in eight massive volumes his Elementa Physiologiae Corporis Humani (Physiological Elements of the Human Body). The work described the advances in physiology made since the time of William Harvey, enriched with Haller's own experimental researches.

Before Haller, physiology followed the views of René Descartes – that bodily systems are essentially mechanical but require some vital principle to overcome their initial inertness. Haller, anticipated somewhat by Francis Glisson, broke radically with this tradition. When stimulated, muscles contract; such ‘irritability’, according to Haller, is inherent in the fiber and not caused by external factors.

The implications of this work were not immediately apparent to Haller. It was left to the philosophers of the Enlightenment to hammer home the conclusion that if such an inherent force resided in muscles then there no longer remained a need for the assumption of vital principles to imbue them with activity.

Haller also made important contributions to embryology and was a noted botanist, publishing a major work on the Swiss flora. However, his attempt to construct an alternative classification scheme to that of Linnaeus, based on fruits rather than sexual organs, received little support despite being a more logical system.