The primary aim of this study was to investigate the outcomes of two different modes (active and passive) of balloon dilatation therapy on cricopharyngeal dysfunction (CPD). Thirty-eight CPD patients with neurological disorders were recruited between 2006 and 2010. Twenty-one of them received active balloon dilatation therapy, and the remaining 17 received passive dilatation therapy for an average of 4 weeks. The patients’ swallowing function before and after the intervention was evaluated using the Functional Oral Intake Scale (FOIS) and the upper esophageal sphincter (UES) opening was studied with the videofluoroscopic swallow study. Both modes of balloon dilatation therapy yielded improvements in the FOIS (active group: z = −3.767, p < 0.001; passive group: z = −3.472, p < 0.001) and the UES opening (both groups: p < 0.01). Active dilatation showed a significantly better FOIS result (p = 0.028) than passive dilatation for CPD. Both active and passive balloon dilatation benefits patients with neurological disorders but active balloon dilatation is better.