Enriching soil carbon storage is regarded as a viable option for mitigating greenhouse gas (GHG) emissions in the agricultural sector. Carbon sequestration by applying biomass into the soil can be an effective sequestration pathway for agriculture. Biochar, charcoal produced from biomass pyrolysis, is highly stable against microbial decomposition, and applying this to farmland has the potential to mitigate GHG emissions. However, CO₂ is emitted throughout the biochar life cycle, including pyrolysis, transportation, and farmland application. Therefore, estimating the net carbon sequestration potential by considering these CO₂ emissions is important. To this end, operational data from a pilot sugarcane bagasse carbonisation plant were collected, and the net carbon sequestration potential with farmland application of bagasse charcoal was calculated using inventory data from the pilot plant. The results were as follows: (i) kerosene consumption during the carbonisation process was the greatest contributor to CO₂ emissions within the life cycle of applying bagasse charcoal to farmland; (ii) the initial dryness of the feedstock was an important factor in estimating net carbon sequestration potentials; (iii) the CO₂ mitigation potential with farmland application of bagasse charcoal on Miyako Island would be 1200–1800 t CO₂/year.