The land use sector is a crucial pillar in achieving the EU climate goals set for 2050. A significant part of the climate change mitigation potential of the land use sector is inherent to agroforestry. Windbreaks are important agroforestry elements of Hungarian agricultural landscapes. The new and improved agroforestry subsidy system may positively affect the extension of windbreaks in Hungary, making it relevant to assess their carbon sequestration potential. In our study, we examined the carbon sequestration of windbreaks at the country level and in two sample areas of 24,000 hectares based on National Forestry Database volume stock data, as well as information collected from the Hungarian Forest Cover Map using orthophoto interpretation. We estimated the total annual carbon sequestration realized in the aboveground biomass pool of Hungarian windbreaks to be −33.1 ktCO2/year, which is 0.67% of the total annual carbon sequestration of the aboveground biomass pool of all Hungarian forests, as reported by the Hungarian Greenhouse Gas Inventory. On the other hand, according to our estimate, the weighted mean annual carbon sequestration in the aboveground biomass of windbreaks was −2.4 tCO2/ha/year in the 2010–2020 period. This value is very close to the average mean annual carbon sequestration per hectare value of all forests, as reported by the Hungarian Greenhouse Gas Inventory. This means that planting a given area of windbreaks in between agricultural fields can have similar climate change mitigation effects as planting forests in the same given area.