The purpose of this blind-assessor randomized crossover trial was to evaluate the effect of Vojta therapy (VT) and a balance training program (BTP) on dynamic sitting balance in individuals with thoracic chronic motor complete spinal cord injury (SCI). Eleven individuals with SCI (T2-T12, American Spinal Injury Association (ASIA) class A-B) were randomly assigned to undergo either VT or BTP for 45 minutes. One week later, the interventions were alternated. The primary outcome measures were dynamic sitting balance assessed via the modified Functional Reach Test (mFRT) and the ability to don and doff a T-shirt (the T-shirt test). Gross motor function assessment (GMFA) was the secondary outcome. All assessments were performed immediately before and after the intervention. The Mann-Whitney U test was used to compare the change score between interventions, and the Wilcoxon signed rank test was used to analyze the data within an intervention. There was not significance difference at before between interventions. VT was superior to BTP in yielding a statistically significant difference in dynamic sitting balance and gross motor function (p-value < 0.05). However, both interventions proved effective in improving dynamic sitting balance and gross motor function (p-value < 0.05) in those suffering from motor complete chronic SCI. A 45-minute VT and BTP program was able to improve dynamic sitting balance and gross motor function relating to the functional ability and activities daily living of individuals with thoracic SCI with a long post-injury time.