Abstract Background Malaria fever is a common medical presentation and diagnosis in Malawi. The national malaria policy supports self-diagnosis and self-medication for uncomplicated malaria with first line anti-malaria drugs. While a qualitative appreciation of the burden of malaria on the health system is recognized, there is limited quantitative estimation of the burden malaria exacts on the health system, especially with regard to human resources and financial burden on Malawi. Methods The burden of malaria was assessed based on estimated incidence rates for a high endemic country of which Malawi is one. Data on the available human resources and financial resources committed towards malaria from official Malawi government documents and programme reports were obtained. The amount of human and financial resources that would be required to treat 65% or 85% of symptomatic malaria cases as per the Roll Back Malaria partnership and the US President's Malaria Initiative targets. Results Based on a malaria incidence rate of 1.4 episodes per year per person it was estimated that there would be 3.71 million symptomatic episodes of malaria among children <5 years of age based on mid-2007 census projections. At 0.59 episodes each year per person there would be 2.13 million episodes in the 5 to 14 year age group and 1.02 million episodes in. There would be 761,848 malaria cases when HIV is not factored in among those 15 years of age or above; this figure rose to 2.2 million when the impact of HIV in increasing malaria incidence was considered. The prevalence of HIV has resulted in 42.3% increase in symptomatic malaria cases. Treating 65% to 85% of cases would result in using 8.9% to 12.2% of the national health budget or 22.2% to 33.2% of the national drug budget. Furthermore, having 65% to 85% of cases treated at a health facility would consume 55.5% to 61.1% of full-time equivalents of all the clinicians registered in the country. While this study's estimated time of 5 and 10 minutes per consultation may differ in actual practice, due to time constraints patients may not be seen for longer consultation in resources limited settings. Conclusion Malaria exacts a heavy toll on the health system in Malawi. The national recommendation of self-medication with first-line drug for uncomplicated malaria is justified as there are not enough clinicians to provide clinical care for all cases. The Malawi Ministry of Health's promotion of malaria drug prescription including other lower cadre health workers may be justified.