A temperature controller shipper for shipping temperature sensitive products. A plurality of individual product boxes contained in an inner mastercase each include a lyophilized product with low thermal mass. The plurality of product boxes each contain a unique PCM thermal dunnage insert occupying the normally empty space within the product box. The PCM insert artificially increases the thermal mass within each product box, and the added thermal mass enables an outer volume of thermal material, e.g. a PCM bladder or bricks, to be minimized to reduce the overall shipper volume and weight.