To improve the accuracy of seismic hazard analysis, understanding the uncertainty of the prediction of the ground-motion amplitude for a specific site owing to a specific source is important. In this study, the variability of the acceleration response spectra of single-path ground motion was evaluated using record pairs obtained from two earthquakes at the same site with the same magnitude, location, and focal mechanism, recorded by high-density strong-motion observation networks in Japan. The natural log standard deviations of the single-path ground motions varied with the period and were distributed in the range of approximately 0.3–0.5. Even if an empirical ground-motion prediction model that accurately models the characteristics of single-path ground motions could be developed, avoiding this variability in the prediction is difficult. The standard deviation of the within-event residuals was smaller at larger distances, and the period of the maximum standard deviation tended to increase as the earthquake magnitude increased. These features may be attributed to differences in the source characteristics of each earthquake. These findings will be useful for the development of advanced empirical ground-motion models and for improving the accuracy of seismic hazard analysis.