Neisser was born in Schweidnitz (now Swidnica in Poland), the son of a physician. He was educated at Munsterberg and at Breslau, where he qualified in medicine (1877) and held the professorship of dermatology (from 1882).

In 1879 Neisser discovered the gonococcus, the causative agent of gonorrhea, which was named for him (Neisseria). In the same year he also identified the bacillus Mycobacterium leprae as the cause of leprosy, but in this he had been anticipated by Armauer Hansen. Neisser also worked on syphilis and collaborated with August von Wasserman in 1906 on the development of his diagnostic test.