Plyometric exercise has been suggested for knee injury prevention in sports participation, but studies on ankle plyometric training are limited. This study aims to investigate the change of joint position sense and neuromuscular activity of the unstable ankle after six-week integrated balance/plyometric training and six-week plyometric training. Thirty recreational athletes with functional ankle instability were allocated into three groups: plyometric group (P) vs. plyometric integrated with balance training group (BP) vs. control group (C). Ankle joint position sense, integrated electromyography (EMG), and balance adjusting time during medial single-leg drop-landing tasks were measured before and after the training period. Following the six-week period, both training groups exhibited a lower absolute error in plantar flexion (P group: pre: 3.79° ± 1.98°, post: 2.20° ± 1.31°, p = 0.016; BP group: pre: 4.10° ± 1.87°, post: 2.94° ± 1.01°, p = 0.045), and the integrated group showed a lower absolute error in inversion angles (pre 2.24° ± 1.44° and post 1.48° ± 0.93°, p = 0.022), and an increased integrated EMG of ankle plantar flexors before landing. The plyometric group exhibited a higher integrated EMG of the tibialis anterior before and after landing (pre: 102.88 ± 20.93, post: 119.29 ± 38.33, p = 0.009 in post-landing) and a shorter adjusting time of the plantar flexor following landing as compared to the pre-training condition (pre: 2.85 ± 1.15 s, post: 1.87 ± 0.97 s, p = 0.006). In conclusion, both programs improved ankle joint position sense and muscle activation of the ankle plantar flexors during single-leg drop landing. The plyometric group showed a reduced adjusting time of the ankle plantar flexor following the impact from drop landing.