This study investigated the effectiveness of Ai Chi compared to conventional water-based exercise on balance performance in individuals with chronic stroke. A total of 20 individuals with chronic stroke were randomly allocated to receive either Ai Chi or conventional water-based exercise for 60 min/time, 3 times/week, and a total of 6 weeks. Balance performance assessed by limit of stability (LOS) test and Berg balance scale (BBS). Fugl-Meyer assessment (FMA) and gait performance were documented for lower extremity movement control and walking ability, respectively. Excursion and movement velocity in LOS test was significantly increased in anteroposterior axis after receiving Ai Chi (p = 0.005 for excursion, p = 0.013 for velocity) but not conventional water-based exercise. In particular, the improvement of endpoint excursion in the Ai Chi group has significant inter-group difference (p = 0.001). Both groups showed significant improvement in BBS and FMA yet the Ai Chi group demonstrated significantly better results than control group (p = 0.025). Ai Chi is feasible for balance training in stroke, and is able to improve weight shifting in anteroposterior axis, functional balance, and lower extremity control as compared to conventional water-based exercise.