In a system for automatically controlling a gear transmission wherein an actuator device coupled with an operation member for the gear-shifting operation of the transmission is controlled for shifting the transmission to a target gear position, the system is provided with a first control unit for producing target signals indicating target gear positions and transmission data showing the relationships between specific gear positions of the gear transmission and positions of the operation member. A second control unit responsive to the target signal and the transmission data to produce a control signal for controlling the actuator device so as to position the operation member to a position corresponding to the target gear position.