A vessel operation system includes an outboard motor or other propulsion apparatus on a hull, an electrically-driven trolling motor mounted externally to the hull, and a controller configured or programmed to control the outboard motor and the trolling motor. The outboard motor generates a thrust and electric power with an engine. The trolling motor generates a thrust by being driven by electric power from a battery that is charged by the electric power generated by the outboard motor. In a state in which the trolling motor is generating the thrust, the controller is configured or programmed to control the outboard motor so as to generate an assist thrust that hastens a behavior of the hull by the thrust generated by the trolling motor.