In a wide range of laser applications, the optical losses of optical materials used in the laser systems are closely linked to the laser-induced damage and laser beam quality deterioration. It is demonstrated in this paper that when the pulsed cavity ring-down (CRD) technique is employed to measure the optical loss of uncoated substrates inserted in the ring-down cavity with normal incidence, the surface reflection of the uncoated substrate causes a significant overestimation of the optical loss. The degree of overestimation increases rapidly with the increasing surface reflectance. By taking into consideration the influence of the surface reflection on the measured CRD signal and developing an approximately linear dependence of the measured loss on the actual loss, the actual loss of the solid substrate is determined accurately from the measured loss. A theoretical description is developed to establish a simple relationship between the CRD measured loss and the actual loss, so to eliminate the influence of the surface reflection on the optical loss measurement. Experimentally the optical losses of fused silica and KDP substrates with 10 mm thickness at 355 nm are determined to be 116 parts per million (ppm) and 567 ppm, respectively. The results demonstrate the usefulness of pulsed CRD for accurate determination of optical loss below the measurement limit (∼3000 ppm) of spectrophotometry.