A cell culture apparatus includes: a supply unit that supplies a culture medium to a culture tank accommodating the culture medium and cells; a discharge unit that discharges the culture medium and the cells from the culture tank; and one or more processors comprising hardware, the one or more processors being configured to determine whether or not cell density in the culture medium in the culture tank has exceeded a preliminarily set predetermined threshold, wherein in response to determining that the cell density has exceeded the predetermined threshold, the one or more processors are configured to cause the discharge unit to discharge a portion of the culture medium and the cells from the culture tank and cause the supply unit to supply a new culture medium to the culture tank to reduce the cell density to the predetermined threshold or less.