The current study was designed to compare long-term clinical outcomes and costs between video-assisted thoracoscopic surgery (VATS) and transcatheter Amplatzer occlusion (TAO). This study enrolled 294 patients with isolated patent ductus arteriosus (PDA) from April 2002 to April 2007, and 290 of these patients were followed up until April 2010. Of the 294 patients, 196 underwent VATS and 98 accepted TAO for PDA closure. The two groups were similar in terms of demographics and preoperative clinical characteristics. No cardiac deaths occurred in either group. All the patients in the VATS group had successful PDA closure, and 94 patients (94/98, 95.9%) in the TAO group had successful PDA occlusion. The incidence of acute procedure-related complications recorded was 1.5% in the VATS group compared with 10.2% in TAO group (P < 0.05). The cost per patient was $1,309.40 ± $312.20 in the VATS group and $3,415.80 ± $637.30 in the TAO group (P < 0.05). There were no cardiac deaths or newly occurring arrhythmias in either group during the fellow-up period. Up to the latest follow-up, no late recanalization or residual shunting was documented, and heart structure returned to normal level in the VATS group. However, residual shunting was detected in four more TAO patients. This study confirmed the long-term safety and efficacy of VATS clipping of PDA. Compared with TAO, PDA interrupted with VATS can achieve both excellent clinical results and satisfying cost effectiveness. The cost for VATS is only a little more than one third the cost for TAO.