The sub-Saharan region of Africa is endemic for malaria, and fever is often assumed to be malaria. In Ghana, about 3.7 million cases were reported in 2011, with 24.4% of these laboratory-confirmed. Other causes of febrile illness, including respiratory syncytial virus (RSV), are prevalent in developing countries like Ghana. There is very little data on the prevalence of this virus in the country. This study determined the proportion of acute febrile illness in an urban paediatric population that was due to malaria or RSV. A hospital based surveillance system recruited children below five years of age reporting with fever (axillary temperature ≥ 37.5°C) at the outpatient department of an urban hospital from February 2009 to February 2010. Consenting parents/guardians were interviewed, the medical history of the child was taken and the child clinically examined. Thick blood film from capillary blood taken through a finger prick, was Giemsa-stained and microscopically examined for malaria parasites to confirm malaria diagnosis. Nasopharyngeal aspirate was also examined for RSV by polymerase chain reaction. Out of 481 febrile children, 51(10.8%) were positive for malaria whilst 75 (15.4%) were positive for RSV. Seven of the 75 RSV-positive cases (9.3%) were co-infected with malaria. Based on judgement by clinicians, over 80% of the febrile children were diagnosed and treated as having malaria either alone or in combination with other diseases. Not all febrile episodes in malaria-endemic regions are due to malaria. The diagnosis and subsequent treatment of patients based solely on clinical diagnosis leads to an over diagnosis of malaria. Improvement in the guidelines and facilities for the diagnosis of non-malaria febrile illness leads to improved malaria diagnosis. Clinicians should be looking for other causes of fever rather than treating all fevers as malaria.