The impact of fire on daily discharges from two mountainous basins located in the permafrost region of Eastern Siberia, the Vitimkan (969 km²) and Vitim (18 200 km²) rivers, affected by fire over 78% and 49% of their areas, respectively, in 2003, was investigated. The results of hydrological and meteorological data analysis suggest that the Vitimkan River basin had a rapid and profound hydrological response to wildfire in 2003 expressed through a 41% (133 mm) increase of summer flow. Conversely, the larger Vitim River basin showed no significant changes in discharge after the fire. The parameters of the process-based hydrological model Hydrograph were estimated for pre-fire conditions. The results of runoff simulations conducted for the continuous pre-fire periods of 1966–2002 and 1970–2002 for the Vitimkan and Vitim river basins, respectively, on a daily time step, showed satisfactory agreement with the observed flow series of both basins. Significant underestimation of precipitation and its poor representativeness for mountainous watersheds was revealed as the main cause of observed and simulated flow discrepancies, especially for high flood events. The set of dynamic parameters was developed based on data analysis and post-fire landscape changes as derived from a literature review. The model was applied to investigate the processes in the soil column and their effect on runoff formation during the post-fire period. The new set of model parameters implied the intensification of soil thaw, reduction of infiltration rate and evapotranspiration, and increase of upper subsurface flow fraction in summer flood events following the fire. According to modelling results, the post-fire thaw depth exceeded the pre-fire thaw depth by 0.4–0.7 m. Total evapotranspiration reduced by 40% in summer months, while surface flow increased almost 2.5 times during maximum flood events.