He became an associate professor at the Hôpital du Val-de-Grâce in 1936, where he directed the chair of epidemiology as well as the phtisiology department of the Percy military hospital.

[1] During the Second World War, he took over the management of the hygiene and epidemiology services of the French Armed Forces and then, in 1941, was appointed Inspector General of Public Health.

[1] Present by chance in Algiers when the allied troops arrived in 1942, he joined them and became the civilian health officer for the liberated territories.

[4] When INSERM was created, an offshoot of the National Institute of Hygiene headed by Louis Bugnard,[5][6][3] he took over its first management in 1964[7] and laid all the foundations for the administrative operation and the objectives of the new institute which turned no longer just towards prevention and statistical studies,[8] but now essentially towards research in biology and medicine.

Aujaleu ended his career as State Councillor and representative of France at the World Health Organization until 1982.