Kocher, an engineer's son from Bern in Switzerland, graduated in medicine from the university there in 1865. He later studied surgery in Berlin, Paris, and in London under Joseph Lister, and in Vienna under Theodor Billroth. Kocher served as professor of clinical surgery at the University of Bern from 1872 until his retirement in 1911 although he continued as head of the University surgical clinic until his death.

Using the antiseptic techniques developed by Lister, Kocher, following the initiative of Billroth, played an important role in developing the operation of thyroidectomy for the treatment of goiter, a not uncommon complaint in Switzerland. By 1914 Kocher was able to report a mortality of only 4.5% from over 2000 operations.

Earlier however, Kocher discovered that while technically successful the operation was responsible for the unnecessary ruin of many lives. In 1883, he found to his horror that something like a third of his patients who had undergone thyroidectomy were suffering from what was politely termed operative myxedema; they had in fact been turned into cretins once the source of the thyroid hormone (thyroxine) had been removed. Kocher showed that such tragedies could be prevented by not removing the whole of the thyroid, for even a small portion possesses sufficient physiological activity to prevent such appalling consequences.

For this work Kocher was awarded the 1909 Nobel Prize for physiology or medicine.