Abstract Siberia experienced an unprecedented strong and persistent heatwave in winter to spring of 2020. Using bottom–up and top–down approaches, we evaluated seasonal and annual CO₂ fluxes of 2020 in the northern hemisphere (north of 30 °N), focusing on Siberia where the pronounced heatwave occurred. We found that, over Siberia, CO₂ respiration loss in response to the pronounced positive winter temperature anomaly was greater than in previous years. However, continued warming in the spring enhanced photosynthetic CO₂ uptake, resulting in the largest seasonal transition in net ecosystem CO₂ exchange; that is, the largest magnitude of the switch from the net CO₂ loss in winter to net CO₂ uptake in spring until June. However, this exceptional transition was followed by the largest reduction in CO₂ uptake in late summer due to multiple environmental constraints, including a soil moisture deficit. Despite a substantial increase of CO₂ uptake by 22 ± 9 gC m⁻² in the spring in response to the heatwave, the mean annual CO₂ uptake over Siberia was slightly lower (3 ± 13 gC m⁻²yr⁻¹) than the average of the previous five years. These results highlight the highly dynamic response of seasonal carbon fluxes to extreme temperature anomalies at high latitudes, indicating a seasonal compensation between abnormal uptake and release of CO₂ in response to extreme warmth that may limit carbon sink capacity in high northern latitudes.