The present work aims toward the effect of uncertain structural parameters on the stochastic dynamic response of an asphaltic lining dam-foundation system subjected to stationary as well as non-stationary random excitation. Uncertain structural parameters of interest are shear modulus and mass density, modeled using the lognormal distribution. The stochastic seismic response of the dam-foundation system to the random loads with uncertain structural parameters is carried out with the Monte Carlo simulation method. The spatial variability of ground motion is considered with incoherence and wave passage effects as stationary as well as non-stationary random excitation. A time-dependent frequency response function is used throughout the study for non-stationary responses. Obtained results indicate that the variability of shear modulus and mass density can be neglected in stochastic dynamic analysis of an asphaltic lining dam-foundation system. Also, it is seen from the results that stationarity is a reasonable assumption for asphaltic lining dams to typical durations of strong shaking.