Inverse analysis is widely used in geotechnical problems, among others, to search a set of input parameters that best fits the observations of a certain model. However, the solutions of an inverse problem are always affected by uncertainties associated with parameter determination, which should be considered simultaneously to the variability of geotechnical data. This paper focuses on the uncertainty analysis of material properties on the responses of Falling Weight Deflectometer tests. A dynamic backcalculation model and a number of sensitivity indices based on Monte Carlo simulation techniques (i.e. Fourier amplitude sensitivity test, FAST) are presented. The dynamic backcalculation is carried-out in the time domain and the inverse procedure is solved by minimizing a relative absolute objective function that involves the peak deflections. Although focus is placed on uncertainties in subgrade material properties, the methodology presented in the paper can be used to quantify uncertainties associated with other layer properties and pavement responses.