With the ability to diagnose malaria with rapid diagnostic tests (mRDT), interest in improving diagnostics for non-malarial fevers has increased. Understanding how health providers diagnose and treat fevers is important for identifying additional tools to improve outcomes and reduce unnecessary antibiotic prescribing, particularly in areas where access to laboratory diagnostics is limited. This study aimed to understand rural health providers’ practice patterns, both quantitatively and qualitatively, and influences on diagnostic and treatment decision making. A mixed methods study was conducted in Mulanje and Phalombe districts in southern Malawi. Retrospective data on diagnoses and treatments of febrile illness from seven mobile clinic logbooks were collected for a two-month period in both the dry and wet seasons. Mobile health clinics visited remote villages in southern Malawi once every seven days. Records from all patients with a recorded axillary temperature of 37.5º C or higher or reported history of fever within 48 hours, and a negative mRDT were included in the analysis. Key informant interviews were conducted with 31 mobile clinic health workers who triage, diagnose, and treat patients as well as dispense medication. In total, 30,672 febrile patients were seen during the study period. Of those, 9,924 (32%) tested negative for malaria by mRDT. Acute respiratory infection was the most common diagnosis for mRDT-negative patients (44.6%), and this number increased in the rainy season as compared to the dry season (OR= 2.18, CI= 2.01, 2.36). Over half (60%) of mRDT-negative patients received antibiotics as a treatment. Almost all the health providers in this study reported limited training in non-malarial fever management, despite the fact that roughly 30% of all patients with fever seen at the mobile clinics tested negative by mRDT. Without diagnostic tools beyond mRDTs, providers relied heavily on patient history to guide treatment decisions.Additional simple to use diagnostic tests as well as additional training in patient examination and clinical assessment are needed in rural settings where health providers risk overprescribing antibiotics or missing a potentially dangerous infection in febrile patients who test negative for malaria.