A method and apparatus for automatically controlling a header lift system of an agricultural harvesting machine, particularly a windrower, to put a header of the machine into a transport mode wherein the header is raised to an elevated transport position, under certain specific conditions. Such conditions can include, but are not limited to, the machine operating in a high-speed range, the header not operating, the speed of the machine being above a predetermined level, and the last inputted control command being a header raise command. When in the transport mode, the lift system can also be operated in a float mode. Further, the header lift system can be returned to a normal mode when certain criteria are present for doing so.