This paper proposes estimation model of uncertainty in vibration measurement of shipboard equipment and analyzes the result of uncertainty estimation. Vibration of shipboard equipments affects underwater radiated noise that is important performance related to stealth of the naval vessel. Acceptance testing for shipboard equipment is required to guarantee the stealth performance of naval vessel. In measuring, detailed uncertainty estimation is essential to improve measuring reliability. Acceptance testing result of structure-borne noise and vibration is used to analyze uncertainty in vibration measurement of shipboard equipment.