In an apparatus for controlling operation of an outboard motor having an internal combustion engine, a transmission and a low-speed cruise controller controlling a rotational speed of the propeller to make the boat cruise at low speed, the low-speed cruise controller outputs an increase/decrease command of the propeller rotational speed in response to an operator's manipulation, and change the gear position from the second speed to the first speed when the decrease command is outputted under a condition where the gear position is in the second speed and an engine speed is equal to or lower than a predetermined speed. With this, it becomes possible to decrease the propeller rotational speed to the maximum extent, thereby making a boat cruise at very low speed.