To provide a controller capable of facilitating changing of the order of robot cells, a control system, and a ladder program. A master PLC includes a master input unit that receives a first input signal indicating the order of operation of robot cells, and a second input signal indicating work completion in the robot cells from each of the plurality of robot cells; a master output unit that outputs an output signal for instruction of operation to the robot cell specified on the basis of combination of the first input signals, and the second input signal according to the ladder program; and a storage unit that stores a plurality of the ladder programs corresponding to a plurality of patterns of the order of operation comprising at least some of the plurality of robot cells.