In 1967, the Defence Council approved the formation of CANEX and shortly thereafter, in 1968, CANEX commenced business. For the next 22 years, CANEX operated under local management, with policy direction emanating from National Defence Headquarters (NDHQ).

In March of 1990, CANEX was restructured as a line organization, operating as a field unit of the ADM(HR-Mil). The NPP Board of Directors, which provides overall direction, is chaired by the Chief of Defence Staff and includes representatives from each of the CF Commands.

In order for CANEX facilities to obtain the lowest possible costs, buying is coordinated through the Merchandise and Marketing department located in Ottawa, which also provides technical support in areas such as food services, advertising/promotions and grocery/convenience stores.