In an apparatus for controlling operation of an outboard motor having an internal combustion engine to power a propeller, and a transmission being selectively changeable in gear position to establish speeds including a first speed and a second speed and transmitting power of the engine to the propeller with a gear ratio determined by established speed, engine speed is detected, it is determined whether acceleration is instructed when the second speed is established, and operation of the transmission is controlled to change the gear position from the second speed to the first speed when the acceleration is determined to be instructed, and then change back the gear position from the first speed to the second speed based on the detected engine speed, thereby enabling to control the transmission optimally.