Eugen Fischer studied medicine, folklore and history in Berlin, Freiburg im Breisgau and Munich from 1893 to 1898. He qualified as Doctor of Medicine in the latter year and in 1890 also qualified as lecturer in anatomy and anthropology at the University of Freiburg. In 1906 he was already a professor (of medicine, anthropology and eugenics) at the University of Freiburg and in 1918 became director of the Anatomical Institute there. From 1927 to his retirement in 1942 he was the director of the Kaiser Wilhelm Institute of Anthropology, Human Heredity and Eugenics. In 1933 he was appointed also as rector of the Frederick Wilhelm University (now Humboldt University) in Berlin. In addition to many scientific papers his publications include the following books and monographs: Die Variationen an Radius und Ulna des Menschen (The variations in the human radius and ulna; Zeitschrift fuer Morphologie und Anthropologie, 1906); Anthropologie (editor, with G. Schwalbe, 1923); Rasse und rassenentstehung beim menschen (Races and their origin among humans, 1927); Das antike weltjudentum (The world Jewry of antiquity; with G. Kittel, 1943); Begegnungen mit Toten: aus den Erinnerungen eines Anatomen (Encounters with the dead: From the recollections of an anatomist, 1959).
In 1908 Fischer came to German South West Africa (now Namibia) to conduct field research among the Rehoboth Bastards, a small group of mixed race people from the Cape Colony who had settled at Rehoboth (some 80 km south of Windhoek) in 1870. His findings were reported in an extensive publication, Die Rehobother Bastards und das Bastardierungsproblem beim Menschen: anthropologische und ethnographische Studien am Rehobother Bastardvolk in Deutsch-Suedwest-Afrika (The Rehoboth Bastards and the problem of miscegenation among humans: Anthropological and ethnographic studies of the Rehoboth Bastard people in German South West Africa; Jena, 1913). He expressed himself against racial intermixing and in favour of the prohibition of racially mixed marriages. This and later studies by him served as part of the scientific basis for racial discrimination by the Nazis.
Fischer retained an interest in South West Africa until long after his retirement, as shown by some of his later papers: "Neue Rehobother Bastardstudien" (Zeitschrift fuer Morphologie und Anthropologie, 1938); "Vor fuenfzig Jahren in SWA zur Erforschung der menslichen Erblehre" (Fifty years ago in SWA for research in human heredity; Journal of the SWA Scientific Society, 1958/9); and "Ist 'Veldkost' immer und Ueberall nur pflanzlicher Herkunft" (Is food from the veld always and only of vegetable origin?; SWA Scientific Society Newsletter, 1966). In this last article he argued that the meaning of the term "Veldkost" should be extended to include animal as well as plant material.