Method and system are provided for controlling a scalable panel cooling system having multiple cooling panels for cooling heat-generating components housed in a support structure. The method includes: dividing the support structure into areas, each area of the support structure capable of housing a heat-generating component; for each area of the support structure: providing a cooling panel adjacent the area of the support structure; determining whether the area of the support structure is housing an operational heat-generating component; in the case that the area of the support structure is housing an operational heat-generating component, activating the cooling panel adjacent the area of the support structure housing the operational heat-generating component; and in the case that the area of the support structure is not housing a operational heat-generating component, deactivating the cooling panel adjacent the area of the support structure.