An apparatus for preventing an inflow of dust in a rear rail of a sunroof may include a rear rail of a sunroof; a tilt lever which has one end portion coupled to a moving glass and the other end portion positioned on the rear rail, and slides along a trajectory of the rear rail; a tilt lever shoe which is positioned at the other end portion of the tilt lever, and configured to be fastened by being fitted with the rear rail; and at least one guide rail which is positioned at the rear rail in a width direction of a vehicle, in which the tilt lever shoe is positioned to surround upper and lower portions of the guide rail, and the guide rail is configured to be sealed to prevent dust from flowing into the rear rail.