Agricultural subsidies have been provided by the Kenyan government to farmers since 2004 in order to increase their outputs thereby improving the economic viability of small-scale farmers and improving food security Access and use of farm inputs in Alego Usonga is wanting as certified seeds and fertilizers are very expensive and out of reach for most farmers in the study area. This study examines the influence of farm inputs subsidy on yields of small holder farmers in Alego Usonga sub-county in Siaya County. The aim of this study is determining how inputs subsidies influence yields of small holder farmers in the study area. The study targeted 317 beneficiary farmers under the government’s subsidy programme in Alego Usonga Sub County. Simple Random Sampling was then used to pick the final samples from the population strata. The instruments for data collection were observation, interview schedule, key informant guide and a structured questionnaire. Data were analyzed using the Statistical Package for Social Science (SPSS) computer program. Quantitative data was analyzed using simple statistics like frequency distribution tables and percentages, while narrative analysis was done using chi-square test for independence, spearman rank correlation to test the nature of the correlation between two variables and logistic regression model. The key findings showed that 55.5% of participants were female while 44.5% were male. Majority 62.1% of the participants agreed to have benefited from input subsidy. 61.5% of the participants agreed that fertilizers subsidy improve crop production. Finally, the study concluded that indeed input subsidy increase yields of small holder farmers.