Internal tides are crucial in ocean dynamics and are a source of error in marine acoustic measurements. In Global Navigation Satellite System-Acoustic combination technique (GNSS-A) seafloor crustal deformation observations, which contribute to earthquake and plate subduction sciences, the effect of internal tides has never been estimated, even though it has been predicted. In this study, we used data from the GNSS-A observation network around Japan to quantitatively identify the effect of internal tides on GNSS-A observations for the first time and reveal the mechanism of the effects of the horizontal wavelength, mode, and direction of internal tides. Long-term sound speed disturbances during GNSS-A observations were generally explained by a semidiurnal internal tide in modes 1 to 3. In future, these results are expected to contribute to progress in multidisciplinary research, such as the construction of advanced physical models and analytical methods.