The cost of accessing healthcare can be a major determinant of disease prevalence, which in turn has short- and long-term welfare implications on poor households. In response, governments in developing countries often resort to subsidizing the cost of drugs, which, while perhaps easier to administer, may not always be the most effective way of addressing healthcare cost. In this regard, we analyze the impact of different types of household level health expenses on disease incidence and agricultural production efficiency. We use data from the 2006 Uganda National Household Survey, which covered approximately 7,400 households. The results suggest that a 10% increase in consultation, medicine, and hospitalization expenses would reduce malaria incidence respectively by 35.6%, 20.5%, and 21.3 %, which translates into a 1.1%, 0.6%, and 0.6 % decrease in agricultural inefficiency, respectively. The results indicate that helping poor households meet expenses for consultation through subsidies or eliminating consultation fees has a larger impact on malaria incidence and agricultural productivity among poor rural households than subsidizing the cost of medical drugs, the most common avenue chosen by developing country governments in the fight against the disease.