Noreen became a student at Uppsala University in 1871 and went on to complete his doctorate there in 1877; he became a lecturer at the university in the same year. Noreen spent most of 1879 at the University of Leipzig, the home of the Neogrammarian school of linguistics - a school to which Noreen belonged for his entire literary life. Whilst in Leipzig, Noreen was taught Lithuanian by August Leskien, a pioneer of research into sound laws.
Much of Noreen's early output was focused on Swedish dialectology, primarily in his home province of Värmland and the neighbouring province of Dalarna. His work, which was the first in Sweden to utilise the findings of the Neogrammarians, remained influential in the field well into the 20th century. Noreen's academic focus in the 1880s shifted to the field of historical linguistics, primarily centred on the Germanic languages. His grammars of Old West Norse and Old Swedish remain in use by scholars to the present day. In 1887 Noreen was named as the third Professor of Scandinavian languages at Uppsala University. Noreen devoted the last twenty years of his life to writing Vårt språk (Our Language), an ultimately unfinished work in which he outlines his view of the Swedish language, its grammar, phonology and morphology. Noreen was elected to Seat 12 of the Swedish Academy in 1919, following the death of Gustaf Retzius.