In 1934 he was appointed as professor at the University of Oslo. He is well known in the Nordic countries for his textbook Lærebok i organisk kjemi. The first modern Norwegian textbook in organic chemistry, it was first released in 1942 and then re-released several times, the last in 1964. The 1958 edition became known for introducing new Norwegian-language names of several chemical elements: hydrogen, nitrogen, karbon (carbon) og oksygen (oxygen).
During the occupation of Norway by Nazi Germany, his academic career was interrupted. When the Nazi authorities were about to change the rules for admission to the university in autumn 1943, a protest ensued. In retaliation, the authorities arrested 11 staff, 60 male students and 10 female students. The staff Johannes Andenæs, Eiliv Skard, Johan Christian Schreiner, Harald Krabbe Schjelderup, Anatol Heintz, Odd Hassel, Ragnar Frisch, Carl Jacob Arnholm, Bjørn Føyn and Endre Berner were sent to Grini concentration camp. Berner was first incarcerated at Berg concentration camp from 22 November 1943, then at Grini until 24 December 1944.
After the war Berner continued as professor at the University of Oslo until 1962, except for a stay at the Imperial College London from 1954 to 1955. He was also active as a professor emeritus until his death. He was elected as a member of the Royal Norwegian Society of Sciences and Letters in 1927, of the Norwegian Academy of Science and Letters in 1933 and of the Society of Chemical Industry in 1951. In 1959, he earned the Nansen medal for Outstanding Research  and in 1969 he was decorated with the Order of St. Olav. He was the president of the Norwegian Chemical Society from 1946 to 1950, having co-founded the Trondheim branch of the society, and ultimately received honorary membership.