Provided is a cell culture apparatus including a cell supply unit that supplies cells; a culture medium supply unit that supplies a culture medium; an additive supply unit that supplies an additive for inducing the differentiation of undifferentiated cells; a stirring unit that stirs a processing target; a separation unit that separates a component contained in the processing target; a culture vessel that cultures the cells; a first flow channel that forms a circulation route passing through the cell supply unit, the stirring unit, the separation unit, and the culture vessel; a second flow channel that connects the culture medium supply unit and the first flow channel; a third flow channel that connects the additive supply unit and the first flow channel; and a control unit that controls the feeding of liquid through the first flow channel, the second flow channel, and the third flow channel.