Haller's attention had been directed to the profession of Medicine while he was residing in the house of a physician at Biel after his father's death in 1721. While still a sickly and excessively shy youth, he went in his sixteenth year to the University of Tübingen (December 1723), where he studied under Elias Rudolph Camerarius Jr. and Johann Duvernoy. Dissatisfied with his progress, he in 1725 exchanged Tübingen for Leiden, where Boerhaave was in the zenith of his fame, and where Albinus had already begun to lecture in anatomy. At that university he graduated in May 1727, undertaking successfully in his thesis to prove that the so-called salivary duct, claimed as a recent discovery by Georg Daniel Coschwitz (1679–1729), was nothing more than a blood-vessel. In 1752, at the University of Göttingen, Haller published his thesis (De partibus corporis humani sensibilibus et irritabilibus) discussing the distinction between "sensibility" and "irritability" in organs, suggesting that nerves were "sensible" because of a person's ability to perceive contact while muscles were "irritable" because the fiber could measurably shorten on its own, regardless of a person's perception, when excited by a foreign body. Later in 1757, he conducted a famous series of experiments to distinguish between nerve impulses and muscular contractions.

Haller then visited London, making the acquaintance of Sir Hans Sloane, william Cheselden, John Pringle, James Douglas and other scientific men; next, after a short stay in Oxford, he visited Paris, where he studied under Henri François Le Dran and Jacob Winslow; and in 1728 he proceeded to Basel, where he devoted himself to the study of higher mathematics under John Bernoulli. It was during his stay there also that his interest in botany was awakened; and, in the course of a tour (July/August, 1728), through Savoy, Baden and several of the cantons of Switzerland, he began a collection of plants which was afterwards the basis of his great work on the flora of Switzerland. From a literary point of view the main result of this, the first of his many journeys through the Alps, was his poem entitled Die Alpen, which was finished in March 1729, and appeared in the first edition (1732) of his Gedichte. This poem of 490 hexameters is historically important as one of the earliest signs of the awakening appreciation of the mountains, though it is chiefly designed to contrast the simple and idyllic life of the inhabitants of the Alps with the corrupt and decadent existence of the dwellers in the plains.

In 1729 he returned to Bern and began to practice as a physician; his best energies, however, were devoted to the botanical and anatomical researches which rapidly gave him a European reputation, and procured for him from George II in 1736 a call to the chair of Medicine, anatomy, botany and surgery in the newly founded University of Göttingen. He became a Fellow of the Royal Society in 1743, a foreign member of the Royal Swedish Academy of Sciences in 1747, and was ennobled in 1749.

Notwithstanding all this variety of absorbing interests, Haller never felt at home in Göttingen; his untravelled heart kept on turning towards his native Bern, where he had been elected a member of the great council in 1745, and in 1753 he resolved to resign his chair and return to Switzerland.

Haller made important contributions to botanical taxonomy that are less visible today because he resisted binomial nomenclature, Carl Linnaeus's innovative shorthand for species names that was introduced in 1753 and marks the starting point for botanical nomenclature as accepted today.

"Not one single physician, as far as I know, during the previous two thousand five hundred years, thought of this so natural, so absolutely necessary and only genuine mode of testing medicines for their pure and peculiar effects in deranging the health of man, in order to learn what morbid state each Medicine is capable of curing, except the great and immortal Albrecht von Haller. He alone, besides myself, saw the necessity of this (vide the Preface to the Pharmacopoeia Helvet., Basil, 1771, fol., p. 12); Nempe primum in corpore sano medela tentanda est, sine peregrina ulla miscela; odoreque et sapore ejus exploratis, exigua illiu dosis ingerenda et ad ommes, quae inde contingunt, affectiones, quis pulsus, qui calor, quae respiratia, quaenam excretiones, attendum. Inde ad ductum phaenomenorum, in sano obviorum, transeas ad experimenta in corpore aegroro," etc. But no one, not a single physician, attended to or followed up this invaluable hint."

About 1773 the state of his health meant he withdrew from public Business. He supported his failing strength by means of opium, on the use of which he communicated a paper to the Proceedings of the Göttingen Royal Society in 1776; the excessive use of the drug is believed, however, to have hastened his death.

Haller, who had been three times married, left eight children. The eldest, Gottlieb Emanuel, attained to some distinction as a Botanist and as a Writer on Swiss historical bibliography (1785–1788, 7 vols). Another son, Albrecht was also a Botanist.