National greenhouse gas emission inventories have consistently highlighted the significant contribution of livestock to national emissions. To date, most noannex 1 countries in Africa, including Rwanda, have relied on default Tier 1 emission factors for livestock because of the absence of country-specific data. However, the present study has taken a step toward rectifying this gap by identifying country-specific emission factors for livestock in Rwanda via the Tier 2 approach outlined in the IPCC 2006 guidelines. The study involved the creation and review of crucial activity data required for Tier 2 calculations. These included data related to the structure of the livestock population; regional distribution by species; various production system types and their respective proportions; daily feed intake; volatile solids; nitrogen excretion; and the types and proportions of manure management systems for cattle, goats, sheep, swine, rabbits and poultry. The population-weighted methane emission factors for enteric fermentation were 62.5 kg/animal per year for cattle and 8.6 kg/animal per year for sheep. These values were higher than the default values stipulated in the Tier 1 IPCC guidelines but fell below the values previously utilized in the Rwanda Biennial Update Report (BUR 1) on greenhouse gas emissions to the United Nations Framework on Climate Change Convention. The data collected did not allow full Tier-2 emission factor calculations for goats, swine, poultry and rabbits. With respect to manure management systems, the reported emission factors for methane and nitrous oxide were notably greater, ranging from 3–26 times greater than the default values set forth in the IPCC 2006 guidelines for Africa. This disparity may be attributed to Rwanda’s zero-grazing policy and predominantly inadequate manure management facilities, with 46% of these facilities being open pits.