Accurate estimation of precipitation in mountain catchments is challenging due to its high spatial variability and lack of measured ground data. Weather radar can help to provide precipitation estimates in such conditions. This study investigates the differences between measured and radar-estimated daily precipitation in the mountain catchment of the Jalovecký Creek (area 22 km2, 6 rain gauges at altitudes 815–1900 m a.s.l.) in years 2017–2020. Despite good correlations between measured and radar-based precipitation at individual sites (correlation coefficients 0.68–0.90), the radar-estimated precipitation was mostly substantially smaller than measured precipitation. The underestimation was smaller at lower altitude (on average by –4% to –17% at 815 m a.s.l.) than at higher altitudes (–35% to –59% at 1400–1900 m a.s.l.). Unlike measured data, the radar-estimated precipitation did not show the differences in precipitation amounts at lower and higher altitudes (altitudinal differences). The differences between the measured and radar-estimated precipitation were not related to synoptic weather situations. The obtained results can be useful in preparation of more accurate precipitation estimates for the small mountain catchments.