Various nondestructive evaluation methods concerning the stress wave through-transmission method have been studied. The propagating velocity and attenuation of a stress wave depend on the material properties of the medium. While ultrasonic wave velocity has been widely used for estimating the elastic modulus of materials, ultrasonic wave attenuation is related to damage in the media. However, in the case of the through-transmission wave method for ultrasonic wave attenuation measurement using contact-type sensors, the amplitude of the measured ultrasonic signal is significantly affected by various external factors such as contact force, system setup, specimen surface condition and ultrasonic couplant. Therefore, in this study, a nondestructive evaluation technique using the self-compensating frequency response function is proposed to measure quantitative ultrasonic wave attenuation in cement-based materials. The proposed technique is able to measure the inherent attenuation of a material, not its relative attenuation. Measurement of inherent attenuation is possible using this experimental setup because the unbiased attenuation is self-compensated with a signal measured at PZT ceramic components inserted between a conventional transducer and the sample in order to except the transducer coupling condition. The reproducibility of the proposed technique is validated by an experimental comparison of conventional measurement and the proposed ultrasonic wave attenuation measurement using concrete and cement paste. Finally, the relevancy of the proposed technique is also validated through testing of damaged cement-based samples.