The Global Fund to Fight AIDS, Tuberculosis and Malaria is the major funaer Of the National Malaria Control Program in Papua New Guinea (PNG). One of the requirements of a Global Fund grant is the regular and accurate reporting of program outcomes and impact. Under-performance as well as failure to report can result in reduction or discontinuation of program funding. While national information systems should be in a position to provide accurate and comprehensive information for program evaluation, systems in developing countries are often insufficient. This paper describes the five-year plan for the evaluation of the Global Fund Round 8 malaria grant to PNG (2009-2014) developed by the Papua New Guinea Institute of Medical Research (PNGIMR). It builds on a complementary set of studies including national surveys and sentinel site surveillance for the assessment of program outcomes and impact. The PNGIMR evaluation plan is an integral part of the Global Fund grant. The evaluation program assesses intervention coverage (at individual, household and health facility levels), antimalarial drug efficacy, indicators of malaria transmission and morbidity (prevalence, incidence), and all-cause mortality. Operational research studies generate complementary information for improving the control program. Through the evaluation, PNGIMR provides scientific expertise to the PNG National Malaria Control Program and contributes to building local capacity in monitoring and evaluation. While a better integration of evaluation activities into routine systems would be desirable, it is unlikely that sufficient capacity for data analysis and reporting could be established at the National Department of Health (NDoH) within a short period of time. Long-term approaches should aim at strengthening the national health information system and building sufficient capacity at NDoH for routine analysis and reporting, while more complex scientific tasks can be supported by the PNGIMR as the de facto research arm of NDoH.