Atrioventricular junction ablation (AVJA) combined with biventricular (BiV) pacing (AVJA/BiV) is an effective treatment for refractory atrial fibrillation (AF) and rapid ventricular response (RVR) associated with heart failure (HF). This study compared the outcomes between patients with non-ischaemic (DCM) and ischaemic cardiomyopathy (ICM) following AVJA/BiV for AF/RVR. This was a retrospective study of 45 patients, comparing the response to AVJA/BiV in patients with ICM to those with DCM. The study compared (a) the change in echocardiographic parameters of HF (ejection fraction (EF) and left ventricular dimensions) prior to, and at least 6 months post AVJA/BiV; and (b) HF hospitalizations (HFH) and appropriate implantable cardioverter defibrillator (ICD) therapies occurring post-procedure. Ejection fraction improved significantly in the DCM group (ΔEF 11.2% ± 11.9; P< 0.01); however, EF remained unchanged (ΔEF 0.5% ± 9.9; P = NS) in the ICM group post-AVJA/BiV. Post-procedurely, HFH were significantly more common (15/18 vs. 4/25; P < 0.0001), and there were significantly more appropriate ICD therapies (9.4 ± 12.3 vs. 2.3 ± 6.1; P = 0.01) in the ICM compared with the DCM group. After AVJA/BiV, there was significantly less post-procedural echocardiographic reverse remodelling, and more HFH in the ICM compared with the DCM group. In addition, significantly more appropriate ICD therapies occurred in ICM patients post-procedure. These differences may be due to the presence of more extensive discrete myocardial scar in patients with ICM. Furthermore, it is possible that tachycardia-induced cardiomyopathy plays more of a causative role in HF in patients with AF and DCM than those with ICM.