Boreal forests nowadays act as a sink for atmospheric carbon dioxide; however, their sequestration capacity is highly sensitive to weather conditions and, specifically to ongoing climate warming. Extreme weather events such as heavy rainfalls or, conversely, heat waves during the growing season might perturb the ecosystem carbon balance and convert them to an additional CO2 source. Thus, there is an urgent need to revise ecosystem carbon fluxes in vast Siberian taiga ecosystems as influenced by extreme weather events. In this study, we focused on the soil CO2 pulses appearing after the rainfall events and quantification of their input to the seasonal cumulative CO2 efflux in the boreal forests in Central Siberia. Seasonal measurements of soil CO2 fluxes (both soil respiration and net soil exchange) were conducted during three consecutive frost-free seasons using the dynamic chamber method. Seasonal dynamics of net soil exchange fluxes demonstrated positive values, reflecting that soil respiration rates exceeded CO2 uptake in the forest floor vegetation layer. Moreover, the heavy rains caused a rapid pulse of soil emissions and, as a consequence, the release of additional amounts of CO2 from the soil into the atmosphere. A single rain event may cause a 5–11-fold increase of the NSE flux compared to the pre-rainfall values. The input of CO2 pulses to the seasonal cumulative efflux varied from near zero to 39% depending on precipitation patterns of a particular season. These findings emphasize the critical need for more frequent measurements of soil CO2 fluxes throughout the growing season which capture the CO2 pulses induced by rain events. This approach has inevitable importance for the accurate assessment of seasonal CO2 soil emissions and adequate predictions of response of boreal pine forests to climatic changes.