Anthropometric indicators are frequently used to monitor children’s nutritional and health status. This study investigated whether the 2007 WHO growth reference inflates estimates of severe malnutrition in children with sickle cell anemia (SCA) compared to a reference tailored specifically for this population. We evaluated children aged 5–12 years with SCA from northern Nigeria enrolled in the SPRING trial (Primary Prevention of Stroke in Children with SCA in sub-Saharan Africa), comparing the prevalence of severe malnutrition (BMI Z-score <−3) and its relationship with mean hemoglobin levels and abnormal transcranial Doppler (TCD) velocities (>200 cm/s) using both references. A total of 799 participants were analyzed (median age 8.2 years, interquartile range 6.4–10.4). Application of the WHO reference produced lower average BMI (−2.3) than the SCA-specific reference (−1.2; p < 0.001) and indicated a markedly higher rate of severe malnutrition (28.6 percent vs. 6.4 percent; p < 0.001). These results reveal that the WHO reference substantially overestimates severe malnutrition in children with SCA. Notably, severe malnutrition, whether defined by the WHO or SCA-specific reference, was not associated with reduced hemoglobin levels or abnormal TCD findings.