A control system for a machine is disclosed. The control system may have a bypass passage situated to allow fluid to bypass an actuator, and a warmup valve disposed within the bypass passage that is movable between flow-passing and-blocking positions. A controller is configured to move the warmup valve to the flow-passing position, fix a displacement position of the pump, compare the pressure of the fluid of the actuator with a threshold, and move the warmup valve to the flow-blocking position and reduce a pump outlet pressure when the pressure of the fluid is greater than the threshold. The controller may be configured to move the warmup valve to the flow-passing position, fix a displacement position of the pump, and adjust an input speed of the pump in response to the signal.