There is not a very simple cause and effect relationship between health of farm workers, malaria, and revenue earned from agriculture. Our study was designed to understand this relationship, including all possible factors affecting agricultural output like malaria, sanitation conditions, socio economic status (SES), availability of health facilities, and the role of gender. Simultaneous equation modeling (SEM) was done to grab the underlying relationships. For assessing SES, a wealth index was created by using principle component analyses (PCA). To create the sanitation and availability of health facility indices we used multiple correspondence analysis (MCA). Results show that improvement in sanitation conditions and socio economic status have direct effects on probability of the occurrence of malaria. More investment on preventive measures and ensuring the availability of health facilities can lessen the disease burden in malaria-endemic areas that indirectly lead to the active participation of economically active members of the family. Our findings suggest that investment in women’s education and farmers’ training with particular focus on malaria can lead to an improvement in farmers’ health that will ultimately result in quality production and increase revenue from agriculture.