Brunner came from a family of Swiss physicians and pharmacists, among whom was Johann Conrad Brunner.[2] His father, John Brunner, was a physician and botanist.[2] Brunner received medical degrees from the University of Zurich and the University of Leipzig, and went on to receive an advanced academic degree of Doctor of Medicine in 1885.[2] He then completed his practical surgeon training studying under Rudolf Ulrich Krönlein.[2] Beginning in 1888 he took a series of trips to noted surgeries, studying under Theodor Billroth at the University of Vienna, Ernst von Bergmann at Humboldt University of Berlin, and other surgeons at the University of Leipzig, the University of Dresden and the University of Münich. In 1888, with the third volume in 1889, he published his Erfahrungen und Studien über Wundinfektion und Wundbehandlung.[3]