Objective The objective of this study is to determine the epidemiological effectiveness of a first-line antiretroviral regimen with HIV protease inhibitor for preventing recurrent malaria in children under the range of HIV prevalence levels and malaria transmission intensities encountered in sub-Saharan Africa. Design A dynamic model of malaria transmission was developed using clinical data on the protease inhibitor extended posttreatment prophylactic effect of the antimalarial treatment, artemether-lumefantrine, in addition to parameter estimates from the literature. Methods To evaluate the benefits of HIV protease inhibitors on the health burden of recurrent malaria among children, we constructed a dynamic model of malaria transmission to both HIV-positive and HIV-negative children, parameterized by data from a recent clinical trial. The model was then evaluated under varying malaria transmission and HIV prevalence settings to determine the health benefits of HIV protease inhibitors in the context of artemether-lumefantrine treatment of malaria in children. Results Comparing scenarios of low, intermediate and high newborn HIV prevalence, in a range of malaria transmission settings, our dynamic model predicts that artemether-lumefantrine with HIV protease inhibitor based regimens prevents 0.03–0.10, 5.2–13.0 and 25.5–65.8 annual incidences of malaria per 1000 children, respectively. In addition, HIV protease inhibitors save 0.002–0.006, 0.22–0.8, 1.04–4.3 disability-adjusted life-years per 1000 children annually. Considering only HIV-infected children, HIV protease inhibitors avert between 278 and 1043 annual incidences of malaria per 1000 children. Conclusion The use of HIV protease inhibitor based regimens as first-line antiretroviral therapy for HIV is an effective measure for reducing recurrent malaria among HIV-infected children in areas where HIV and malaria are coendemic, and artemether-lumefantrine is a first-line antimalarial.