Purpose This study aimed to investigate the effect of eccentric training of trunk muscles on muscle activation and balance in patients with stroke. Methods The study participants consisted of 32 patients diagnosed with stroke who met the inclusion criteria for this study. They were randomly assigned into two groups: 16 in the study group and 16 in the control group. The study group performed eccentric training of trunk muscle, while the control group performed trunk stabilization exercise. Both groups engaged in these exercise for 30 minutes once a day, three times a week, for a duration of five weeks. Dependent variable measures based on the intervention were surface Electromyography(sEMG) for muscle activation, Trunk impairment scale(TIS) for trunk control, and Berg balance scale(BBS) and Timed up and go(TUG) for balance. Results There were significant differences between study group and control group in sEMG, TIS, TUG, whereas there were no significant differences between study group and control group in BBS. There was also a significant between-group difference in balance abilities. Conclusion The eccentric training of the trunk muscles presented in this study has a positive effect on improving muscle activation, trunk control, and balance during functional movement in patients with stroke.