Postmor tem next-generation sequencing (NGS) plays a crucial role in uncovering previously unidentified genetic causes of death. It provides essential findings useful for counseling affected family members and advancing our understanding of genetic diseases. In this report, we present the first documented autopsy case of hypertrophic cardiomyopathy (HCM) in South Korea in which postmortem NGS was used to identify a novel mutation. A 40-year-old male with no relevant medical history experienced sudden death at home. The autopsy revealed cardiac findings consistent with HCM but no other potential causes of sudden death. Through postmortem NGS analysis, a novel pathogenic mutation, c.2833_2834del, in MYBPC3 gene, was discovered; hence, this serves as the first report of this mutation in a Korean population. This finding not only confirms the diagnosis of HCM but also provides a plausible explanation for the sudden death. Given the hereditary nature of HCM, genetic counseling is strongly recommended, especially for the deceased’s nine-year-old son, who has a 50% risk of inheriting the mutation. This case underscores the critical role of postmortem NGS in the field of forensic medicine. The significance of NGS and necessity for integration into autopsy investigations are highlighted.