As a medical doctor, Anavaj worked for ten years in clinical medicine before embarking on a career in basic research. After attaining a PhD in human molecular genetics at Oxford University, he joined the Institut Pasteur in 2000 to develop a program on the human genetics of infectious diseases focusing on arthropod-borne infections including malaria, dengue and Zika.

He coordinated a research network on dengue for the Pasteur Network and is a coordinator of a European FP7 project "Dengue Framework for Resisting Epidemics in Europe" (DENFREE).

He is now a Program Director of Pasteur International Center for Emerging Infectious Diseases (PICREID) as well as a representative and executive director of Fondation Pasteur Japon.