Malaria remains a leading cause of morbidity and mortality among children in sub-Saharan Africa. Acute kidney injury (AKI) is increasingly recognized as a frequent and severe complication of pediatric severe malaria, yet it remains largely underdiagnosed. This under-recognition is driven by important limitations in current diagnostic approaches. The World Health Organization (WHO) criteria rely on fixed serum creatinine (SCr) thresholds that are poorly adapted to children, whereas Kidney Disease Improving Global Outcomes (KDIGO) criteria require baseline SCr (bSCr) values that are rarely available in low-resource settings. The estimation of bSCr using back-calculation methods is further complicated by population-specific factors, particularly malnutrition, which reduces creatinine generation and may mask kidney injury. In addition, urine output (UO) monitoring is often underutilized despite its diagnostic value, and access to laboratory testing remains limited. Emerging biomarkers such as neutrophil gelatinase-associated lipocalin (NGAL), cystatin C, and kidney injury molecule-1 (KIM-1) show promise for early detection and risk stratification but remain insufficiently validated in African pediatric populations. In this narrative review, we highlight key challenges in diagnosing malaria-associated AKI (MAKI) in children and discuss potential strategies to improve early detection in resource-limited settings, with the aim of reducing morbidity and mortality.