Farm input subsidies are assumed to improve agricultural production and productivity for small resource poor farmers in developing countries by promoting the use of improved farm inputs, mainly inorganic fertilizers and hybrid seeds. This is expected to contribute to increased income from produce sales, improved food security at household and national levels, and consequently, contributing to poverty alleviation. However, little insights exist on the impacts of this program. The overall objective of the study was to determine the effect of the fertilizer subsidy program on reducing poverty among small holder farmers in Gatsibo district, Eastern province of Rwanda. Multi stage sampling techniques were employed to select respondents. Structured questionnaires was employed to collect data from 200 smallholders maize farmers including (86 farmers with fertilizer subsidy and 114 without subsidies in the period 2015B, 2016A and 2016B agricultural seasons in the selected sectors of Kabarole, Rwimbogo and Rugarama). Propensity score matching using a “with” and “without” the fertilizer subsidy project evaluation approach was used to estimate the effect of fertilizer subsidy and descriptive statistics using t-test was used compare effects of fertilizer subsidies across respondents. Based on the study objectives, results from propensity score matching indicated an effect on yield between fertilizer subsidy users and non-users.