Background Isolated left ventricular apical hypoplasia (ILVAH) is a rare congenital cardiac abnormality, which might result in severe symptomatic heart failure (HF) with pulmonary hypertension, atrial fibrillation (AF), or malignant ventricular tachycardia in adults. Case summary A 32-years-old man presented with exertional dyspnoea New York Heart Association Class II and persistent AF. Echocardiography and cardiac magnetic resonance showed the presence of (i) spherical remodelling of the left ventricle (LV) with impaired contractile function (three-dimensional ejection fraction, EF 32%); (ii) substitution of apical myocardium by fatty tissue; (iii) abnormal origin of a papillary muscle network; and (iv) an elongated right ventricle, compatible with ILVAH. In addition, non-compacted endomyocardial layer of the LV was observed. Because of a high risk of sudden cardiac death in symptomatic HF patients with reduced EF, an implantable cardioverter-defibrillator was placed which followed by pulmonary vein isolation. After the procedures and restoration of sinus rhythm, the patient demonstrated improvement in HF symptoms and exercise tolerance. This was accompanied by an enhancement of left and right ventricular systolic function by echocardiography. At 6-month, 1, and 2-year follow-up the clinical conditions of the patient and echocardiographic findings remained stable. Discussion A rare combination of ILVAH and left ventricular myocardium non-compaction was observed in this young adult who presented with symptomatic HF and persistent AF. The use of consecutive invasive cardiac procedures leads to restoration of sinus rhythm, the improvement of myocardial contractility and clinical manifestation of HF.