A shift control system for an automatic transmission is provided, which is mounted on a vehicle configured to be started by an ignition switch being turned on, where an automatic transmission mode or a manual transmission mode is selectively set. The system includes a shift switch through which a manual transmission command for arbitrarily changing a gear stage of the automatic transmission can be inputted in the manual transmission mode, and a controller. The manual transmission mode includes a first manual mode in which the gear stage is changed and maintained by inputting the manual transmission command using the shift switch, and a second manual mode in which the automatic transmission mode is resumed by satisfying a resuming condition after the gear stage is changed. When the ignition switch is turned on, the controller selects in advance the second mode to be set to the automatic transmission.