Background: In patients with hypertrophic cardiomyopathy (HCM), borderline left ventricular (LV) ejection fraction (LVEF) was reported to be a significant risk factor for developing LV systolic dysfunction (LVSD), which is associated with poor prognosis. However, the natural history of patients with borderline LVEF and risk factors for progression to overt LVSD are incompletely characterized. Methods: HCM patients who had two or more echocardiography exams between 2005 and 2023 and a borderline LVEF of 50–59% on the initial exam were included. Patients who progressed to LVSD during follow-up were compared with patients with preserved LV systolic function. Results: Among 2,282 HCM patients evaluated, 145 patients (6.4%) with borderline LVEF at baseline were included (median age 61, IQR 51-72; male 67%). Compared to patients with normal LVEF (≥60%), patients with borderline LVEF had more atrial fibrillation (AF) (16% vs. 38%), less obstructive physiology (18% vs. 6.2%), larger left atrial (LA) size, and lower LV global longitudinal strain (LV-GLS) (-16.1 vs. -13.7%) and LA reservoir strain (LARS) (27.7% vs. 21.7%) (all p<0.001). During median follow-up of 6.5 [IQR 3.2–10.9] years, 30 patients (21%) progressed to LVSD. Patients who progressed to LVSD were younger (55 vs. 64 years, p<0.001), had less hypertension, lower LVEF (55% vs. 57%, p<0.001), larger LV and LA dimensions, and higher ESC sudden cardiac death risk scores (2.1% vs. 1.4%, p<0.001) compared to patients with preserved LVEF. They also had lower baseline LARS (18.2% vs 22.6%, p=0.028) and LA contraction strain (9.3% vs. 12.2%, p=0.011), while there were no differences in LV-GLS and LA conduction strain. On multivariable Cox regression analysis, independent predictors of LVSD progression were identified as younger age (HR 0.82, 95% CI 0.70–0.97, p=0.017, per 5 years), lower LVEF (HR 0.80, 95% CI 0.71–0.91, p<0.001), larger LV end-diastolic dimension (HR 1.17, 95% CI 1.06–1.30, p=0.002), and lower LARS (HR 0.94, 95% CI 0.89–0.98, p=0.011). Conclusions: Among HCM patients with borderline LVEF, 21% progressed to overt LVSD. Younger age, lower LVEF, larger LV size and lower LA strain at baseline predicted the development of LVSD.