Achieving climate change mitigation requires precise assessment of agricultural greenhouse gas (GHG) emissions. Although animal husbandry, soil management, and manure systems primarily address emissions generated directly on farms, hidden or unaccounted emissions remain largely unregulated. Agricultural and rural operations produce significant carbon emissions through indirect activities beyond farm boundaries. This review investigates major sources of greenhouse gas emissions linked to agricultural activities. Agricultural input production and transportation emissions, post-harvest storage and distribution losses, rural development infrastructure emissions, degraded land microbiological activity, and poorly managed or abandoned facilities fall under this category This study examines scientific and administrative challenges to evaluating these emissions. The major challenges include inadequate monitoring systems, unclear accountability, and dispersed rural emission sources. New technological tools, such as satellite-based carbon tracking, remote sensing of soil carbon changes, and machine learning techniques for emission detection will improve monitoring and measurement effectiveness. Mitigation approaches involve implementing full-chain life cycle assessments (LCAs), adapting sustainability frameworks to cover farm and post-farm stages, and developing policy tools that encourage emission management across the agricultural supply chain. Agriculture's environmental impact can be more precisely assessed by including these overlooked sources in greenhouse gas inventories. Adopting holistic approaches helps in crafting effective climate policies, enhancing sustainability certification systems, and empowering farmers, researchers, and policymakers to actively contribute to emission reduction. This study concludes that agricultural and rural greenhouse gas emissions evaluation studies should incorporate cross-disciplinary research methods and scalable technologies.