Malaria is one of the commonest tropical diseases plaguing rural African thus combating it has remained a major health and economic issue as highlighted in the Sustainable development Goals (SDGs).This study examined the effect of malaria on the productivity of cassava based farmers in Ogun state. The data for this study were collected from 338 farmers in Ogun State selected using multi-stage sampling techniques. Information gathered, which included socio-economic, institutional and farm-level factors, were analyzed using descriptive statistics, Total Factor Productivity (TFP) and regression model (at Pvalue ? 0.05). The result of the analysis showed that 72% of the farmers were susceptible to malaria. Average days of incapacitation due to malaria in the study area (proxy for malaria burden) were 12 days with estimated average annual per capita income loss of N 10,922.83 (approx. $30). Few farming households (20%) used mosquito nets to prevent malaria and most of them (53%) practice self-medication in treating malaria when sick. Majority (51%) of the farmers had productivity levels >1.0 and their level of productivity is influenced negatively by days of incapacitation due to malaria. Other factors which influenced productivity include level of education, farming experience, farmers’ access to credit facility and farm size. Thus, efforts should be directed towards policies and programmes that will further enhance farmers’ awareness of the need to prevent malaria especially with the use of mosquito nets and environmental sanitation. This will increase their potential to improve productivity sustainably.