Abstract Wildfires in boreal forests release substantial amounts of carbon into the atmosphere. However, current land-surface models are limited in their representation of fire processes, including their ignition and spread. This study thus developed FireDL, a novel data-driven machine-learning model for the prediction of natural wildfires, and combined it with a land-surface model to better understand the impact of fire on carbon fluxes. FireDL has a two-stage deep learning structure that sequentially combines a long short-term memory (LSTM) algorithm and an artificial neural network (ANN). Preliminary random forest analysis identified fire duration as an important factor in predicting the burned area. Thus, in FireDL, the LSTM algorithm was employed to predict fire occurrence and duration, utilizing lightning, vegetation, and climate datasets. Subsequently, the ANN predicted the total burned area using the LTSM-derived fire duration predictions and climate datasets as input. FireDL produced a robust performance in predicting large fires (>10,000 ha), achieving a correlation coefficient of 0.72. The daily-scaled burned area predictions derived from FireDL were integrated into the Community Land Model version 5 – Biogeochemistry (CLM5-BGC) to produce CLM5-BGC-FireDL. This integration considerably improved carbon emission estimations. Notably, the total net ecosystem exchange (NEE) estimated using CLM5-BGC-FireDL in 2019, the year with the highest recorded burned area during our study, was twice that estimated using the standard CLM5-BGC. Discrepancies in the NEE can significantly influence atmospheric CO2 levels, highlighting the importance of our fire prediction model in forecasting the burned area and carbon emissions. The use of FireDL with future climate scenarios is thus anticipated to yield valuable insights into ecosystem management and climate change mitigation strategies.