Accurately predicting displacement is crucial in the design of isolation systems. Rigid mass models, which neglect the superstructure’s flexibility, are commonly used for this purpose due to their simplicity. However, this assumption may compromise accuracy by neglecting the superstructure’s flexibility. This study investigates the validity of the rigid mass model for isolation systems with single friction pendulums by comparing its displacement predictions to those of flexible superstructure models. A comprehensive analysis was conducted on 1720 isolation system models subjected to 245 ground motion records, including both pulse-like and no-pulse motions. Statistical results show that when the stiffness ratio, defined as the ratio of the isolation system’s effective period to the superstructure’s fundamental period, exceeds certain thresholds, the displacement of the isolation system becomes largely independent of the superstructure’s flexibility. Conversely, at lower stiffness ratios, the displacement exhibits significant variability, highlighting the complex interactions between the superstructure and the isolation system. Additionally, the findings reveal that pulse-like ground motions result in lower displacement variability compared to non-pulse motions, and that taller buildings are more sensitive to the effects of superstructure flexibility, despite sharing the same fundamental period.