This study presents site characterization performed for nine strong‐motion stations in the Israeli Seismic Network (ISN). Measurements conducted using the refraction microtremor (ReMi) and multichannel analysis of surface waves (MASW) techniques are compared with previously available velocity profiles from refraction surveys and a horizontal‐to‐vertical spectral ratio (HVSR) study. The linear‐elastic 1D site response is computed for all stations, using all available velocity profiles. Intramethod and intermethod variability of the full velocity profiles, their time‐averaged shear‐wave velocity (), and the calculated amplification functions are discussed and compared. We find that the intermethod variability is significantly higher than the intramethod variability. We also see that the uncertainty associated with the of the profiles (approximately from average) is generally smaller than that associated with specific amplification parameters (e.g., , from average). Finally, in the nine sites we tested, there are no consistent trends that can point to one method being preferable to others; hence, we must accept an amount of epistemic uncertainty.