BACKGROUND: Acute febrile illness is a common reason for seeking healthcare in low- and middle-income countries. We describe the diagnostic utility of a TaqMan Array Card (TAC) real-time polymerase chain reaction (PCR) panel for pathogen detection in paediatric and adult inpatients admitted with febrile illness. METHODS: In this prospective cohort study, we screened medical admissions for a tympanic temperature ≥38.0°C or reported fever within 72 h and used a PCR panel to detect pathogens, including bacteria, viruses, fungi and protozoa, in 697 participants. We compared PCR results to conventional diagnostic methods and considered PCR detections as the cause of fever, except for Plasmodium spp. and Schistosoma spp. Participants for PCR testing was consecutively selected from the end of enrolment. RESULTS: Of 1132 participants enrolled in the cohort, 697 (61.6%) were tested by PCR. Median (IQR) age was 29.6 (4.6-46.4) years. Three hundred seventy-eight (54.2%) were male. The PCR method improved illness identification, increasing diagnostic yield from 73 (10.5%) by conventional methods to 124 (17.8%) of 697 participants. PCR detections included four viral pathogens: dengue (n = 1), enterovirus (n = 7), measles (n = 1) and Rift Valley Fever Virus (RVFV) (n = 3). Forty-six bacterial pathogens were detected in 44 (6.3%) participants, including fastidious bacteria such as Bartonella spp. (n = 2), Brucella spp. (n = 3), Coxiella burnetii (n = 2), Leptospira spp. (n = 1), M. tuberculosis (n = 7) and Rickettsia spp. (n = 9). CONCLUSION: The PCR panel improved pathogen detection in febrile inpatients, providing clinically actionable results for fastidious bacteria and epidemiologically relevant findings like RVFV detections, when combined with conventional methods.