BACKGROUND: 46, XY disorders of sex development (DSD) and aceruloplasminaemia (ACP) are very rare genetic disorders, and no cases of the coexistence of both disorders have been reported. In ACP patients, iron overload in multiple organs leads to progressive dysfunction of those organs. Early recognition of the coexistence of these conditions is challenging, resulting in difficulties in making a prompt diagnosis and determining the appropriate intervention. RESULTS: We present a young female patient who was diagnosed with 46, XY DSD due to primary amenorrhea. One decade later, she was admitted for examination due to abnormally high ferritin levels. After the exclusion of common diseases that can cause an increase in ferritin levels, further examination revealed an increase in liver parenchymal density and markedly low CP levels in the plasma. Whole-exome sequencing (WES) revealed a mutation in the CP gene, and the patient was diagnosed with 46, XY DSD with ACP. Iron overload decreased significantly after treatment with deferasirox (DFS). CONCLUSION: We aimed to improve the understanding of this complex genetic disorder, and clinicians are advised to be aware of the possibility of coexisting chromosomal abnormalities that emphasize the value of genetic testing, especially in patients with atypical presentations. This information is helpful for identifying other potentially comorbid genetic disorders, achieving the implementation of early treatment strategies, and preventing organ damage.