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Introduction: Sierra Leone has one of the highest burdens of febrile illnesses in the world. As the incidence of malaria diminishes, a better understanding of the spectrum of etiological agents was important for accurate diagnosis and empirical treatment of febrile illness. Methods: Blood, nasopharyngeal, and fecal specimens were collected from febrile patients for serological, molecular detection, and microbiologic culture to identify potential pathogens. Results: For this prospective study, 142 febrile patients were enrolled. The prevalence of malaria was higher in children aged 5–15 years old (P = 0.185) and adults (P = 0.018). Acute respiratory infection (ARI) presented more commonly in the under 5 years old group (P = 0.009). For diarrhea, all children groups (P = 0.024) were predominant. A total of 22.5% of the febrile patients had malaria infection, 19.7% had typhoid infection, and 2.8% were coinfected with malaria and typhoid. ARI was the most common causes of fever, accounting for 31.7% of patients, influenza A virus, Mycoplasma pneumoniae, and five other respiratory pathogens were found. Diarrhea accounted for 16.2%, and seven kinds of diarrhea bacteria were isolated. Hepatitis B accounted for 8.5%, including five cases of spontaneous bacterial peritonitis, and ascites smear staining were both Gram-negative bacteria. Tuberculous encephalitis, parasitic diseases (ascaris and filariasis), and skin infection caused by Staphylococcus aureus accounted for 0.7%, 2.1%, and 0.7%, respectively. Conclusions: Evidence of a wide spectrum of febrile etiological agents other than malaria was identified. The spread of malaria rapid diagnostic tests (RDTs) out of hospital and establishment of a national standard for Widal test will reduce the misdiagnosis of febrile diseases. Antibiotics against Gram-negative bacteria are helpful for empirical treatment. Plain Language Summary: Sierra Leone has one of the highest burdens of febrile illnesses in the world. Evidence of a wide spectrum of febrile pathogens other than malaria has been proven in this study. We considered that the etiology of febrile patients was closely related to local geography, heredity, immune features, economic industry, living habits, air pollution, medical and health conditions, and this was fully analyzed and discussed. The screening process used in this study can further simplify and identify the etiological agents of fever in more than 70% of the study population. This laid the foundation for the establishment of a more simplified and efficient diagnosis and treatment process in the local area. We also found the characteristics of age distribution of different febrile diseases. Children were an important susceptible population to fever. This study indicated the importance of reliable diagnostic tests for febrile pathogens and provided the necessary information for RDT requirements. The spread of malaria RDTs out of hospital and establishment of a national standard for Widal test will reduce the misdiagnosis of febrile diseases. For empirical treatment, antimalarial treatment was still targeted at falciparum malaria in Sierra Leone. Antibiotics against Gram-negative bacteria contributed to the empirical treatment of febrile diseases. For patients with acute respiratory tract infection, Gram-positive coccal antibiotics could be candidates for treatment. In addition, systematic and professional treatment of liver diseases should be promoted to reduce infection complications. [ABSTRACT FROM AUTHOR]