A medical system includes: a treatment tool including a treatment portion, a joint portion, a flexible tube portion, and a drive unit； an endoscope device including an outer sheath that holds the treatment tool and an imaging unit that is capable of acquiring an image including at least the joint portion； and a control unit that controls an operation of the treatment tool. The control unit includes a table that has a parameter for causing the joint portion to move, a controller that issues a command for controlling the drive unit based on the parameter to the drive unit, an image processing unit that calculates at least one of a position and an orientation of the joint portion based on the image, and a compensation value calculating unit that detects displacement of the joint portion based on at least one of the position and the orientation of the joint portion calculated by the image processing unit, generates a compensation value for compensating for a difference between the command and the displacement of the joint portion, and incorporates the compensation value into the parameter.
