Background: We combined yoga with standard stroke rehabilitation and compared it to the rehabilitation alone for depression and balance in patients. Methods: Forty patients aged from 30 to 80 who had suffered a stroke 90 or more days previously were divided evenly with age stratification and patients’ will (hence not randomized). In the intervention group 16 completed 8-week stroke rehabilitation combined with 1 h of yoga twice weekly. Another 19 patients completed the standard rehabilitation as the control group. Results: The yoga group showed significant improvement in depression (Taiwanese Depression Questionnaire, p = 0.002) and balance (Berg Balance Scale, p < 0.001). However, the control group showed improvement only in balance (p = 0.001) but not in depression (p = 0.181). Further analysis showed both sexes benefitted in depression, but men had a greater improvement in balance than women. Depression in left-brain lesion patients improved more significantly than in those with right-brain lesion, whereas balance improved equally despite lesion site. For patients under or above the age of 60, depression and balance both significantly improved after rehabilitation. Older age is significantly related to poor balance but not depression. Conclusions: Combining yoga with rehabilitation has the potential to improve depression and balance. Factors related to sex, brain lesion site and age may influence the differences.