Ammonia is one of the precursor gases in the formation of particulate matter (PM) that reacts with nitrogen oxides and sulfur oxides in the atmosphere. Based on the Clean Air Policy Support System (CAPSS) of Korea, the annual ammonia emissions amounted to 261,207 tons in 2020 and the agricultural source (manure management sector) contributes the highest proportion of the ammonia inventory. However, the methodology for the study of ammonia emissions in Korea has some limitations regarding the representativeness of the sites selected and the reliability of the measurement method. In this study, we aimed to recalculate the ammonia emissions from the livestock industry in Korea using the UK’s estimation method, which uses the life cycle assessment of livestock manure. Three major animal types, i.e., cattle (beef cattle and dairy cows), pigs and chickens, and three major processes based on the manure flow, i.e., housing, manure storage and treatment and land application processes, were considered. The total ammonia emissions were estimated to be approximately 33% higher than the official ammonia emissions stated by the CAPSS. For the manure flow, the ammonia emissions were the highest from land application processes. The ammonia emissions from dairy cow and poultry manure were much higher than those stated by the CAPSS, while the emissions from beef cattle and pig manure showed similar levels. The methodology used in this study can offer an alternative approach to the ammonia emission estimation of the manure management sector in the agriculture industry of Korea. Korean emission factors based on the manure flow should be developed and applied in the future.