We explored the effects of 6-week whole-body vibration (WBV) and balance training programs on female athletes with chronic ankle instability (CAI). This randomized controlled study involved female athletes with dominant-leg CAI. The participants were randomly divided into three groups: WBV training (Group A), balance training (Group B), and nontraining (control group; Group C). Groups A and B performed three exercise movements (double-leg stance, one-legged stance, and tandem stance) in 6-week training programs by using a vibration platform and balance ball, respectively. The Star Excursion Balance Test (SEBT), a joint position sense test, and an isokinetic strength test were conducted. In total, 63 female athletes with dominant-leg CAI were divided into three study groups (all = 21). All of them completed the study. We observed time-by-group interactions in the SEBT ( = 0.001) and isokinetic strength test at 30°/s of concentric contraction (CON) of ankle inversion ( = 0.04). Compared with the control group, participants of the two exercise training programs improved in dynamic balance, active repositioning, and 30°/s of CON and eccentric contraction of the ankle invertor in the SEBT, joint position sense test, and isokinetic strength test, respectively. Furthermore, the effect sizes for the assessed outcomes in Groups A and B ranged from very small to small. Female athletes who participated in 6-week training programs incorporating a vibration platform or balance ball exhibited very small or small effect sizes for CAI in the SEBT, joint position sense test, and isokinetic strength test. No differences were observed in the variables between the two exercise training programs.