Haemoglobin (Hb) AE Bart's disease is a rare form of thalassemia that results from the co-inheritance of Hb E and alpha thalassemia, typically with Hb H disease. The clinical severity can vary depending on the underlying genetic mutations, particularly in the presence of Hb Constant Spring (Hb CS), which is a highly unstable form of alpha thalassemia. Understanding the genetic basis and haematological profiles of Hb AE Bart's disease is crucial for proper diagnosis and management. We report the case of a nine-year-old Malay boy presenting with severe hypochromic microcytic anemia, jaundice, and hepatosplenomegaly. Haemoglobin electrophoresis findings consistent with Hb H Constant Spring disease co-inherited with Hb E. Molecular genetic testing confirmed compound heterozygosity for the South East Asian (SEA) deletion and Hb CS mutation along with heterozygous Hb E. This case highlights the importance of considering complex haemoglobinopathies such as Hb AE Bart's disease in patients presenting with anemia, especially in regions with a high prevalence of thalassemia. Early diagnosis through a combination of Hb electrophoresis and molecular genetic testing is essential for proper management and genetic counseling to prevent long-term complications.