Malaria remains a major public health challenge in sub-Saharan Africa, affecting household labor and economic productivity. In agricultural communities, the disease can disrupt farm management and reduce profitability, particularly for labor-intensive crops such as rice. This study investigates the effects of malaria on the management of family rice farms in the urban commune of Gaya. The methodological framework combined descriptive statistics, comparative analyses across rainy and dry seasons, and econometric modeling. Data were collected from 104 rice-farming households. Results demonstrate that both the average number of individuals affected by malaria and the associated healthcare expenditures are substantially higher during the rainy season. In the rainy season, health-related costs markedly increase total production expenses, causing value added and the profitability index to decline sharply (from 0.423 to 0.095). In contrast, during the dry season, despite higher revenues, the impact of health expenditures remains marginal, with only a slight reduction in the profitability index (from 3.26 to 3.22). Econometric analysis further reveals that, in the rainy season, rice farm profitability is significantly and negatively influenced by the number of lost workdays, malaria prevalence, and cultivated area (p<0.05). Each additional workday lost due to malaria reduces farm profitability by approximately USD 93, corresponding to a 3.6% decline relative to baseline profitability. These findings underscore malaria’s dual burden on rice-farming households: it reduces labor availability while increasing financial costs, particularly during the rainy season when labor demands peak. Strategies to mitigate malaria could therefore improve both health and economic outcomes for smallholder rice farmers.