This study reports the geostatistical analysis of a set of 40 single-station horizontal-to-vertical spectral ratio (HVSR) passive seismic survey data collected in the Kathmandu basin (Nepal). The Kathmandu basin is characterized by a heterogeneous sedimentary cover and by a complex geo-structural setting, inducing a high spatial variability of the bedrock depth. Due to the complex geological setting, the interpretation and analysis of soil resonance periods derived from the HVSR surveys is challenging, both from the perspective of bedrock depth estimation as well as of seismic-site effects characterization. To exploit the available information, the HVSR data are analyzed by means of a geostatistical approach. First, the spatial continuity structure of HVSR data is investigated and interpreted taking into consideration the geological setting and available stratigraphic and seismic information. Then, the exploitation of potential auxiliary variables, based on surface morphology and distance from outcropping bedrock, is evaluated. Finally, the mapping of HVSR resonance periods, together with the evaluation of interpolation uncertainty, is obtained by means of kriging with external drift interpolation. This work contributes to the characterization of local seismic response of the Kathmandu basin. The resulting map of soil resonance periods is compatible with the results of preceding studies and it is characterized by a high spatial variability, even in areas with a deep bedrock and long resonance periods.