Overdiagnosis and overtreatment of malaria is a major problem in children in malaria-endemic countries. This retrospective study identified children who were admitted with fever and were treated with or without anti-malarial medications and discharged at the Paediatric Unit of the Effia-Nkwanta Regional Hospital. The medical records of all children were searched, retrieved and assessed. A total of 1160 records from children (age range, 0–12 years) were reviewed and evaluated. Of the total number, 21.3% had laboratory confirmed malaria, 38.4% were malaria negative, while 40.3% had no malaria tests performed. In addition, the results showed that 4.5% of the laboratory confirmed malaria positive cases were not given anti-malarial medication while 84.1% of the malaria negative cases were given these incorrectly. Furthermore, 78.2% of the children with no malaria tests were prescribed anti-malarial medication. The presumptive diagnosis of malaria should be abandoned and the installation of a functional laboratory services promoted.