Abstract Aims The outcomes of patients with hypertrophic cardiomyopathy with left ventricular systolic dysfunction (HCM-LVSD) undergoing left ventricular assist device (LVAD) implantation remain unclear. We retrospectively evaluated the clinical impact of LVAD implantation on clinical outcomes, including haemodynamics and brain natriuretic peptide (BNP) levels, in patients with HCM-LVSD, in comparison with those with dilated cardiomyopathy (DCM). Methods and results In this retrospective, single-centre, observational study conducted in Japan, the medical records of patients who underwent LVAD implantation in the National Cerebral and Cardiovascular Center between 2011 and 2020 were reviewed. We enrolled 96 patients with DCM (average age: 43.5 years; 73 men) and 24 patients with HCM-LVSD (average age: 48.3 years; 16 men). The HCM-LVSD group had smaller left ventricles with thicker ventricular walls than the DCM group, which became more prominent after LVAD implantation. Preoperatively, BNP values were comparable between both groups; however, 3 months post-implantation, they were significantly higher in the HCM-LVSD group. Pulmonary artery pulsatility index, right ventricular stroke work index, and cardiac index were lower, and right atrial pressure was higher, in the HCM-LVSD group, suggesting subclinical impairment of right ventricular function. The HCM-LVSD group demonstrated equivalent outcomes, including overall survival, cerebrovascular accidents, right ventricular failure, LVAD-related infections, arrhythmia, and aortic insufficiency, post-implantation. Conclusions Despite a decreased right ventricular function with higher BNP values, patients with HCM-LVSD and DCM showed comparable outcomes post-LVAD implantation.