A method of setting a medical system, in which at least one treatment tool and at least one manipulation input unit for manipulating the treatment tool are connectable to each other, includes a step of acquiring first information capable of identifying the treatment tool and second information capable of identifying the manipulation input unit, a step of associating the treatment tool with the manipulation input unit on the basis of a comparison between the first information and the second information, and a step of associating an input to the manipulation input unit with an operation of the treatment tool with respect to the manipulation input unit associated with the treatment tool on the basis of the comparison between the first information and the second information.
