He studied anthropology and archaeology in Vienna and there he was most influenced by Robert von Heine-Geldern. He wrote his thesis on the tribal social organization of the peoples of Assam and NW Burma (Staat und Gesellschaft bei den Völkern Assams und des nordwestlichen Birmas) and in later years was inspired by John Henry Hutton, a fellow researcher of the tribal communities in that region.
After his thesis, von Fürer-Haimendorf moved to London in order to establish contact with the main anthropologists of his time, such as Bronislaw Malinowski. By 1936 he traveled to India, where he worked among the Naga people and established good friendships among the local administrators of the British Raj. After five months and great effort, he succeeded in learning the local language and was able to do without an interpreter. From then onwards, von Fürer-Haimendorf would insist that it was of the utmost importance for an ethnologist or ethnographer to learn well the language of the people who were the subject of the fieldwork in order to be competent in his or her studies.
In 1938, von Fürer-Haimendorf married Betty Barnado, a colleague. At the time he only made a brief visit to Europe and returned to India, so that at the outbreak of World War II he found himself in British territory holding a Third Reich passport. He was arrested by the colonial authorities, but with a great degree of politeness and sadness, for they were good friends of his. Thus he was confined to Hyderabad State in South India. As time went by von Fürer-Haimendorf earned the trust of the local authorities, who could see that he had no Nazi sympathies. He was then able to do some of his best fieldwork ever while living among the Chenchu, Bhil, Reddi and the Raj Gond Adivasi of present-day interior Telangana.
Thanks to friendly government officers, which included fellow ethnologist Verrier Elwin, von Fürer-Haimendorf was able to obtain a post as Special Officer and Assistant Political Officer to the North East Frontier Agency, so he could move back to Northeast India. He studied the Apatanis in 1944–45, when there were tensions in the area owing to the Japanese conquest of Burma.
When the war was over von Fürer-Haimendorf was named Advisor for Tribes and Backward Classes to the Nizam's Government of Hyderabad and returned to the South where he continued to do ethnographic fieldwork while he was engaged as government officer. In 1953, when the Kingdom of Nepal opened to the outside world, von Fürer-Haimendorf did not want to lose the opportunity to visit the then little-known country and became the first foreigner who was able to do research among the peoples of Nepal.
Christoph von Fürer-Haimendorf lived his old age in London, where he became professor of anthropology at the School of Oriental and African Studies. In 1987, following the death of his wife, his health suffered a decline from which he did not recover. He died on 11 June 1995 and was buried in London.