A method and system for controlling a horizontal directional drilling machine having a boring tool. A rate of rotation and a rate of thrust are selected by an operator. Controls allow an automatic boring operation mode to be initiated to maintain the selected rate of rotation and thrust without further input from the operator. Periodically, when the rotation and thrust are interrupted, such as to modify the drill string, the automatic boring operation mode is interrupted. The automatic boring operation mode may be resumed without requiring the operator to select the rate of rotation and rate of thrust. The rate of rotation is resumed before the rate of thrust to reduce drill string shock loads and increase drilling performance.