BACKGROUND: Parasitological confirmation is now recommended for all cases of suspected malaria. The roll-out of rapid diagnostic tests (RDTs) is hoped to enable this goal in low resource settings through point of care testing. However, simply making RDTs available has not led to high uptake of the tests or adherence to results by clinicians, with malaria continuing to be overdiagnosed in many settings. We undertook to design an evidence-based intervention package that would be sufficient to support the introduction of RDTs at dispensaries in Tanzania, to be evaluated through the Targeting Artemisinin Combination Therapy (TACT) cluster randomised controlled trial. METHODS: We describe five steps in our intervention design: formative research, review of existing evidence and theory, a workshop to define the intervention approach and content and results of formative research, engagement with behaviour change theory and literature, detailed design of intervention materials and piloting and pretesting of intervention materials. This involved fieldwork with a total of 19 health workers and 212 community members in northeast Tanzania. RESULTS: The formative research suggested that RDTs were a potential source of conflict in the health worker-patient interaction, but that health workers used various techniques to resolve this, including provision of antimalarial drugs for RDT-negative patients. Our reviews showed that evidence was mixed regarding the effectiveness of different methods and theories to support change in prescribing practice. Our design process is presented, drawing from this collective evidence. We describe the final TACT intervention package (including interactive small group workshops, feedback text messages, motivational text messages and patient information leaflets and posters) in terms of its programme theory and implementation theory. CONCLUSIONS: Our study suggests that evidence-based design of complex interventions is possible. The use of formative research to understand malaria overdiagnosis in context was central to the design of the intervention as well as empirical research to test materials and methods prior to implementation. The TACT interventions may be appropriate for other settings where clinicians face similar challenges with malaria diagnostics. TRIAL REGISTRATION: NCT01292707.