Provided is a cell culture apparatus including a culture vessel that stores a cell suspension containing cells; a first filter part that has a first filter membrane that performs membrane separation treatment on the cell suspension extracted from the culture vessel; a first circulation flow path that allows components blocked by the first filter membrane to return to the culture vessel; a second filter part that has a second filter membrane that performs membrane separation treatment on components of the cell suspension permeated through the first filter membrane; a second circulation flow path that allows components permeated through the second filter membrane to return to the culture vessel; and a recovery flow path that recovers components blocked by the second filter membrane. In the cell culture apparatus, an average hole diameter of the first filter membrane is 20 μm or smaller, and 0