The agricultural sector plays a crucial role in addressing food insecurity and malnutrition in developing countries, and smallholder farmers are significant contributors to food production. In Uganda, the National Agricultural Advisory Services (NAADS) program was initiated in 2001 to provide extension services and agricultural input subsidies to farmers. However, the program has faced criticism for its high levels of corruption, militarization, and political influence, as well as for its failure to reach its intended beneficiaries, and smallholder farmers. This paper aims to examine the contribution of smallholder farmers to food security and its sensitivity to agricultural input subsidies in Uganda, with a focus on the NAADS program. Additionally, it covers the evolution of agricultural input subsidy policy in Uganda from 1987 to the present and analyses the findings on the impact of these subsidies on smallholder farmer productivity and food security. The findings conclude that the NAADS program contributes less to the target beneficiaries, and its priorities do not align with the set goals. The study further suggests several recommendations for improving the program and addressing the issues facing smallholder farmers in Uganda.