The institute works closely with the Ministry of Youth and Sports, as well as is the parent institution of Azerbaijan, providing scientific and methodological guidance to sports dispensaries.

In accordance with the set goals, the National Institute of Sports Medicine and Rehabilitation consists of treatment, preventive, scientific and educational structures. Their interaction leads to better coordination and activates horizontal intra-enterprise connections. Management is carried out by the director of the institute and his deputies for medical science and sports.

The institute includes the following departments: