Evidence on the impact of using diagnostic tests in community case management of febrile children is limited. This effectiveness trial conducted in Burkina Faso, Ghana, and Uganda, compared a diagnostic and treatment package for malaria and pneumonia with presumptive treatment with anti-malarial drugs; artemisinin combination therapy (ACT). We enrolled 4,216 febrile children between 4 and 59 months of age in 2009-2010. Compliance with the malaria rapid diagnostic test (RDT) results was high in the intervention arm across the three countries, with only 4.9% (17 of 344) of RDT-negative children prescribed an ACT. Antibiotic overuse was more common: 0.9% (4 of 446) in Uganda, 38.5% (114 of 296) in Burkina Faso, and 44.6% (197 of 442) in Ghana. Fever clearance was high in both intervention and control arms at both Day 3 (97.8% versus 96.9%, P = 0.17) and Day 7 (99.2% versus 98.8%, P = 0.17). The use of diagnostic tests limits overuse of ACTs. Its impact on antibiotic overuse and on fever clearance is uncertain.