In an apparatus for controlling operation of an outboard motor having an internal combustion engine and a transmission 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, it is configured to control operation of the transmission to change the gear position to the first or second speed in response to an outputted speed change command, determine whether an engine speed is continuously equal to or greater than a predetermined speed for a predetermined time period when the speed change command to the first speed is outputted, and when the determination is affirmative, change the gear position from the first speed to the second speed. With this, it becomes possible to mitigate the load on a transmission gear to improve durability of the transmission.