Background Selenium is an integral component of several antioxidant enzymes especially glutathione peroxidase and plays a role in countering oxidative stress. Sickle cell anaemia (SCA) is a genetic disorder characterized by the presence of two mutant haemoglobins (HbSS). Individuals with SCA have chronic oxidative stress even in steady state which predisposes them to selenium deficiency. Method Children aged 1 – 16 years who are attending the Paediatric sickle cell clinic and age and sex matched haemoglobin AA controls were recruited for the study. An interviewer administered questionnaire was used in obtaining information from the participants; their anthropometric parameters were measured while blood was collected for serum selenium levels and Packed Cell Volume. The data was analysed using Statistical Package for Scientific Solutions (SPSS) version 21. Results Children with SCA had a significantly lower serum selenium level than controls(p < 0.0001) The mean serum selenium levels of subjects were lower, though not significantly, in females, lower maternal educational status, lower socioeconomic class, lower haematocrit levels and in stunted and underweight children. Conclusion The mean serum selenium levels of children with sickle cell anaemia were significantly lower than children without sickle cell anaemia and the prevalence of selenium deficiency was very high