Provided is a manipulator system (1) comprising: a manipulator (3) provided with an elongated insertion unit, the manipulator (3) being further provided with a movable unit provided at the distal end of the insertion unit, the manipulator (3) being also provided with a drive unit provided at the proximal end of the insertion unit and driving the movable unit; an operation input unit (5) for inputting an operational input to be applied to the manipulator (3); a control unit (6) for controlling the drive unit on the basis of the inputted operational input; an endoscope; an over-tube (4) having a first channel through which the endoscope is inserted and a second channel through which the manipulator (3) is inserted; and an endoscope rotational angle calculation unit for calculating the angle of offset of the endoscope about the longitudinal axis relative to the first channel. On the basis of the angle of offset, the movable unit is rotated about the longitudinal axis thereof relative to the second channel, thereby aligning the vertical direction of a coordinate system affixed to the endoscope and the vertical direction of a coordinate system affixed to the movable unit.