Objectives: Intra- and interatrial electromechanical delay (AEMD) can be used to evaluate the development of atrial fibrillation (AF). Percutaneous transluminal septal myocardial ablation (PTSMA) is an alternative therapy for patients with hypertrophic obstructive cardiomyopathy (HOCM) that results in sustained improvements in atrial structure and function. We investigated the effects of PTSMA on the intra- and inter-AEMD of HOCM patients using tissue Doppler imaging. Methods: Conventional echocardiographic and AEMD parameters were obtained in 25 healthy controls and 31 HOCM patients before and 1 year after septal ablation procedures. Results: Compared with the healthy controls, the left atrial volumes indexed by body surface area (LAVI) and the intra- and inter-AEMD were significantly higher in the HOCM patients. At 1 year after PTSMA, the LAVI was decreased (37.2 ± 11.4 to 27.0 ± 8.5 ml/m2, p < 0.001). The intra- and inter-AEMD were also significantly decreased (22.7 ± 9.2 to 16.6 ± 7.7 ms, p < 0.001 and 37.0 ± 8.4 to 26.6 ± 8.0 ms, p < 0.001, respectively). These changes correlated well with the reductions in LAVI (r = 0.83, p < 0.001; r = 0.66, p < 0.001). Conclusions: Both the intra- and inter-AEMD were significantly prolonged in the HOCM patients. PTSMA can improve the prolonged and inhomogeneous propagation of sinus impulses in atria.