He studied oriental languages and theology, but soon became interested in natural history.
He contributed his observations of insects to Erik Pontoppidan"s Danske Atlas (1763-1781). After being put in charge of the natural history collection of Christian Fleischer he became interested in ornithology, and in 1764 he published Ornithologia Borealis, which included the details of many Scandinavian birds, some described for the first time. The publication of Ornithologia Borealis was aided by his insight in the collection.
Brünnich corresponded with many foreign naturalists including Linnaeus, Peter Simon Pallas and Thomas Pennant.
He published his Entomologia in 1764. He then embarked on a long tour of Europe, spending time studying the fish of the Mediterranean Sea and publishing his Ichthyologia Massiliensis on the subject in 1768.
On his return Brünnich took up the post of Lecturer in Natural History and Economy at Copenhagen University. Here he established a natural history museum and wrote a textbook for his students, the Zoologiae fundamenta.
Brünnich"s guillemot is named after him.
Royal Danish Academy of Sciences and Letters. Royal Norwegian Society of Sciences and Letters.