Double-chambered right ventricle (DCRV) is a rare congenital heart defect in adults, manifesting with progressive right ventricular outflow tract obstruction. We describe the first case of DCRV coexisting with hypertrophic cardiomyopathy, which is complicated by atrial flutter. A middle-aged woman with recurrent symptomatic atrial flutter who had previously been diagnosed with biventricular hypertrophic cardiomyopathy was admitted to our department. Echocardiography and cardiac magnetic resonance revealed asymmetrical interventricular septal hypertrophy, and abnormal muscle bundles within the right ventricle, generating an obstructive gradient. Genetic testing detected a hypertrophic cardiomyopathy-associated mutation: MYH7, c.4135G > A, p. Ala1379Thr. A diagnosis of DCRV complicated by hypertrophic cardiomyopathy and atrial flutter was made. Surgical intervention was performed, which included radiofrequency ablation, removal of abnormal muscle bundles, and ventricular septal defect repair. Intraoperative transesophageal echocardiography demonstrated the well-corrected right ventricular outflow tract. Free of early postoperative complications, the patient was discharged in sinus rhythm on the 11th day after the surgery. Unfortunately, the patient died from a sudden death 38 days following the surgery. In conclusion, the coexistence of DCRV with hypertrophic cardiomyopathy in patients is an uncommon condition. The present case highlights the importance of diagnostic imaging in the management of this disorder.