A cell observation system observes a cell moving in a flow path with a fluid, and includes a first imaging apparatus, a second imaging apparatus, and a control device. The first imaging apparatus includes a first optical system and a first imaging element, and captures an image of the cell at a first position in a moving direction. The second imaging apparatus includes a second optical system, in which a focus is adjusted based on a focus adjustment signal, and a second imaging element, and captures an image of the cell at a second position downstream of the first position. The control device obtains a passing position of the cell in a cross section of the flow path based on the image obtained by the first imaging element, generates the focus adjustment signal, and provides the signal to the second optical system.