In an apparatus for controlling an outboard motor mounted on a stern of a boat and having an internal combustion engine to power a propeller, a drive shaft that connects the engine and the propeller, a torque converter that is interposed between the engine and the drive shaft and is equipped with a lockup clutch, a water pump connected to the drive shaft to be driven by the drive shaft, and a shift mechanism interposed between the drive shaft and the propeller, comprising a neutral position detector that detects the shift mechanism being set in a neutral position; and a clutch ON unit that makes the lockup clutch ON to increase operation speed of the water pump when it is detected that the shift mechanism is set in the neutral position. With this, it becomes possible to improve cooling performance, thereby preventing a defect such as overheat of the engine.