Hoffmann was a research assistant at CNRS from 1964 to 1968, and became a research associate in 1969. Since 1974 he has been a Research Director of CNRS. Between 1978 and 2005 he was Director of the CNRS research unit "Immune Response and Development in Insects", and from 1993 to 2005 he was director of the Institute of Molecular and Cellular Biology of CNRS in Strasbourg.