An apparatus and method for the batch photoactivation of mononuclear cells (MNCs) is described. The system includes a programmable controller configured to automatically separate whole blood in a first collection cycle to obtain a first quantity of MNCs; separate whole blood in a second collection cycle to obtain a second quantity of MNCs while simultaneously photoactivating the first quantity of MNCs to obtain a first quantity of treated MNCs; either store the first quantity of treated MNCs or reinfuse the first quantity of treated MNCs; photoactivate the second quantity of MNCs to obtain a second quantity of treated MNCs; either store the second quantity of treated MNCs or reinfuse the second quantity of treated MNCs; and reinfuse any blood components remaining after the second collection cycle.