François Jouen's scientific career began in 1980 with a research assistant position at the French Ministry of the Environment, where he studied the effects of noise pollution on postural regulation in children. In 1982, soon after completing his PhD in psychology at University René Descartes Paris 5, he was recruited as a research associate at National Centre for Scientific Research (CNRS) in the Child Psycho-Biology Laboratory of Ecole Pratique des Hautes Etudes (EPHE).
In 1984, he spent several months at the MIT Center for Space Research to further his knowledge of computer science and computer science in system programming.
Appointed research officer at CNRS in 1985, he continued his work on the development of the vestibular system in the Child Psycho-Biology Laboratory until 1991.
In January 1992, he joined the Cognitive Neuroscience and Cerebral Imaging Laboratory at Pitié-Salpêtrière Hospital to work on electrophysiology of the vestibular cortex in humans. From 1995 to 2000, he worked at Laboratory of Neurobiology of Learning at University of Rouen, where he initiated a series of researches on sensori-engine development in the newborn. During this period, he was also interested in the role of the cerebellum in motor control and aging of the motor system in animals.
He joined EPHE as senior researcher in 2001 and took charge as head of EPHE's Developmental Psychobiology Laboratory. The general framework of his research developed at EPHE since 2001 is that of probabilistic epigenesis. This approach involves simulation and modeling computer science.