OBJECTIVES: Malaria imposes a substantial global disease burden with 198 million cases reported worldwide in 2013. It disproportionately affects sub-Saharan Africa, particularly young children and accounts for 14% of the region’s childhood deaths. In an effort to improve disease management, the World Health Organization (WHO) in 2010 recommended countries test children (age < 5) who present with suspected malaria fever and confirm diagnosis rather than treat them presumptively with antimalarial drugs, the standard of care to date. While all 47 African countries designated as malaria-endemic, have adopted the policy, significant barriers to implementation exist.  These include costs, uncertainty about the overall health benefits, shortfalls in testing supplies and physician practice patterns.  METHODS: We use a decision-analytic approach to assess the policy’s cost effectiveness in three countries in sub-Saharan Africa: Angola, Tanzania and Uganda, each representing different prevalence/income combinations. Our model includes country-specific epidemiologic, cost and behavioral data, including that of physician and caregiver.  Our primary data sources are national Malaria Indicator Surveys and information from each country's National Malaria Control Program.  We use a Markov specification to account for multiple fever episodes and estimate the incremental cost-effectiveness of the testing policy through two-stage micro-simulation models.  These models capture key dimensions of uncertainty associated with our projections.  RESULTS: We find that diagnostic testing for malaria is cost-saving in Angola.  In Tanzania the cost per life-year gained is $5.54 and $94.58 in Uganda.  Both are cost-effective compared to the WHO standard of $150 per life-year gained.  Our results are robust under varying cost, prevalence and behavioral assumptions. Probabilistic sensitivity analyses indicate that testing is cost-saving or cost-effective: 80% of the time in Angola, 89% in Tanzania, and 69% in Uganda.  CONCLUSIONS: Our findings strongly suggest pursuit of policies that facilitate full implementation of testing, including promoting clinician adherence to test results.