Malaria is one of the most common tropical diseases affecting both the rural and urban areas in Nigeria. The disease has posed a serious threat to agricultural production and little has been done in terms of general understanding of the effects of malaria on agricultural production. This study therefore attempts to fill this gap by examining the effect of malaria on agricultural production in Yobe State. A Multi-stage sampling technique was employed to select 400 each of malaria infected and uninfected respondents. Descriptive statistics such as frequency and percentage, and inferential statistics such as multiple regression and economic loss model were employed for the analysis. The result showed that malaria infected households had 20% less agricultural output in relation to the uninfected households. The analysis showed that the average days of incapacitation for 2011 was 16.16days, which translated to ₦9, 696.00 and ₦12, 928.00 based on the national daily minimum wage of N600.00 and the local average daily labour wage of N800.00, respectively. The analysis further showed that the average cost of malaria treatmentper person per year was ₦2, 583.08. The result of the regression showed that the coefficients of family labour and house size were positive and significant (P<0.01 and P<0.05, respectively). Furthermore, the coefficients of days of incapacitation, cost of treatment, frequency of and distance to source for malaria treatment were all negative and significant (P<0.01, P<0.001, P<0.001 and P<0.001, respectively), implying that a unit increase in these variables will lead to a decrease in crop output. Among others, the study recommends that malaria control awareness in relation to the impact on agricultural production should be integrated into agricultural extension services in the State.