An operating device for a sunroof of a vehicle may include a motor housing disposed at a rear side of a roof panel and a mounting space, an operating motor disposed at one side of the motor housing and a worm inserted into the mounting space, a gear unit rotatably disposed in the mounting space engaged with the worm and is rotated by the operating motor, a glass cable connected to the gear unit and to a moving glass disposed outside of the roof panel to move the moving glass, a sun shade cable connected to the gear unit at an upper side of the glass cable and is connected to the sun shade inside the roof panel to move the sun shade, and a locking unit disposed on the motor housing corresponding to the gear unit and selectively locks the gear unit such that the cable is separately operated.