Ankle sprain is a common musculoskeletal injury, and recurrent ankle sprains often lead to ankle instability. This study aimed to examine whether a 6-week balance training on a wobble board (WB) combined with kinesio taping (KT) is effective in improving balance, postural stability, and ankle stability among female athletes with functional ankle instability (FAI). Twenty-four female athletes with FAI were randomly assigned to study (SG) or control groups (CG). SG attended a 6-week training protocol of combined balance training on the wobble board with KT applied to ankles during exercise. CG only went through a 6-week balance training procedure that was the same as the SG. Before and after the training program, balance and postural stability and the severity of ankle instability were assessed by single-leg Biodex Balance system and Cumberland Ankle Instability Tool (CAIT), respectively. The analysis revealed that the scores of balance and postural stability decreased after the 6-week training for CG (p = 0.002) and SG (p = 0.001), which indicates an improvement for these variables, and the score of CAIT increased, which means the severity of instability reduced (p = 0.001 for both groups). Significant between-group differences were found for balance and postural stability (t = 2.79, p = 0.011, g = −1.99) and the severity of instability (t = 2.082, p = 0.049, g = 1.36), favoring SG compared with CG. This study showed that the addition of KT to balance training is more effective than balance training alone in improving balance, postural stability, and severity of ankle instability in female athletes with FAI. Our findings could provide a preliminary reference for designing combined balance and KT programs for delivering health benefits to females with FAI.