An apparatus and method for calibrating a PTO for driving a header of an agricultural windrower, wherein a programmable control module in connection with at least signal operated device in operative control of a variable displacement pump operable for controlling operation of the PTO, is programmed as part of an automatic calibration routine for determining values for the control signals required for operating the header at a predetermined target speed for a plurality or range of speeds of an engine driving the pump, such at the pump can be controlled to minimize occurrences of overpumping of fluid and resultant problems.