There is a paucity of data on the etiologies and outcomes of febrile illness in rural Sierra Leone, especially in the Lassa-endemic district of Kenema. We conducted a retrospective study of patients with subjective or documented fever (T ≥ 38.0°C) who were admitted to a rural tertiary care hospital in Kenema between November 1, 2011 and October 31, 2012. Of 854 patients admitted during the study period, 429 (50.2%) patients had fever on admission. The most common diagnoses were malaria (27.3%), pneumonia (5.1%), and Lassa fever (4.9%). However, 53.4% of febrile patients had no diagnosis at discharge. The in-hospital mortality rate was 18.9% and associated with documented temperature ≥ 38.0°C (adjusted odds ratio [AOR] = 2.89, P = 0.001) and lack of diagnosis at discharge (AOR = 2.04, P = 0.03). Failure to diagnose the majority of febrile adults and its association with increased mortality highlight the need for improved diagnostic capacity to improve patient outcomes.