Uncertainties are essential, yet often neglected, information for evaluating the reliability in forest carbon balance projections used in national and regional policy planning. We analysed uncertainties in the forest net biome exchange (NBE) and carbon stocks under multiple management and climate scenarios with a process-based ecosystem model. Sampled forest initial state values, model parameters, harvest levels and global climate models (GCMs) served as inputs in Monte Carlo simulations, which covered forests of the 18 regions of mainland Finland over the period 2015–2050. Under individual scenarios, the results revealed time- and region-dependent variability in the magnitude of uncertainty and mean values of the NBE projections. The main sources of uncertainty varied with time, by region and by the amount of harvested wood. Combinations of uncertainties in the representative concentration pathways scenarios, GCMs, forest initial values and model parameters were the main sources of uncertainty at the beginning, while the harvest scenarios dominated by the end of the simulation period, combined with GCMs and climate scenarios especially in the north. Our regionally explicit uncertainty analysis was found a useful approach to reveal the variability in the regional potentials to reach a policy related, future target level of NBE, which is important information when planning realistic and regionally fair national policy actions.