An apparatus and method for measuring a velocity of a moving object in a navigation system are provided, which can increase an accuracy of velocity measurement and position estimation of the moving object are provided. The apparatus includes a sensor part including an acceleration sensor for measuring acceleration of the moving object and outputting a corresponding acceleration measurement value, and includes an altimeter for measuring an altitude of the moving object and outputting a corresponding altitude measurement value; and a calculation part for calculating the velocity of the moving object by using the acceleration measurement value output from the acceleration sensor and the altitude measurement value output from the altimeter.