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, generates a compensation value, and incorporates the compensation value into the parameter.