[Purpose] The purpose of this study was to examine the effect of virtual reality-based eccentric training on lower extremity muscle activity and balance in stroke patients. [Subjects and Methods] Thirty stroke patients participated, with 15 patients allotted to each of two eccentric training groups: one using a slow velocity (group I) and one using a fast velocity (group II). The virtual reality-based eccentric training was performed by the patients for 30 minutes once a day, 5 days a week, for 8 weeks using an Eccentron system. Surface electromyography was used to measure the lower extremity muscle activity, while a BioRescue was used to measure balancing ability. [Results] A significant difference in lower extremity muscle activation and balance ability was observed in group I compared with group II. [Conclusion] This study showed that virtual reality-based eccentric training using a slow velocity is effective for improving lower extremity muscle activity and balance in stroke patients.