The Stepper Motor Controller provides simple and accurate control of the levels, waveforms, timing and phase-shifts of the current for a two phase stepper motor via SAE J1939 command messages. Analog and Digital command inputs are provided for a run-time parameter, feedback in a PID control loop or as an E-stop command. 1 pulse or PWM input for inductive or active sensor is available. Motor direction is selectable. An additional output is provided, a sinking digital output (up to 5A) for a relay, brake or other load.