An apparatus and method are provided for controlling a powertrain of an autonomous vehicle. The apparatus includes an autonomous driving controller that controls autonomous driving of the vehicle and a transmission controller that determines whether the vehicle satisfies a pulse and glide (P&G) driving condition during the autonomous driving. The transmission controller alternately performs pulse driving and coasting in conjunction with the autonomous driving controller when the vehicle satisfies the P&G driving condition. The transmission controller causes a transmission to remain in a neutral state during the coasting.