We aimed to implement strength and balance training for elite adolescent male soccer players with functional ankle instability (FAI) to assess kinesiophobia, ankle instability, ankle function, and performance. This cluster randomized controlled trial comprised 51 elite adolescent male soccer players with FAI recruited from six different teams, divided into strength, balance, and control groups (SG, n = 17; BG, n = 17; and CG, n = 17, respectively). The SG and BG underwent strength and balance training sessions three times per week for 6 weeks. Primary outcomes were the Tampa scale for kinesiophobia-17 (TSK) and Cumberland ankle instability tool (CAIT) scores to assess kinesiophobia and FAI, respectively. Secondary outcomes were ankle strength (four directions), dynamic balance, static balance (ellipse, displacement, velocity), and performance (figure 8 and side-hop tests). A significant interaction effect was observed for both TSK and CAIT post-intervention (both, P < 0.01). In post hoc analyses, the BG had significantly better outcomes in reducing TSK. The SG and BG showed greater improvements in CAIT scores. Regression analysis indicated that CAIT severity correlated significantly with TSK (P = 0.039, R = 0.289). For secondary outcomes, the SG and BG were superior in terms of ankle dorsiflexion/inversion strength, static balance displacement, and figure-8 and side-hop tests (all, P < 0.05). The BG showed significantly better static balance ellipse results (P < 0.05). The 6-week intervention significantly enhanced kinesiophobia management, ankle stability, and performance. Balance training effectively mitigated kinesiophobia and improved balance, compared with strength training alone. Even small variations in CAIT severity can influence kinesiophobia, highlighting the potential benefits of balance training. Integrating balance training into training programs can address both physical and psychological aspects of ankle instability. Research is recommended to explore the longitudinal effects of these interventions and their potential to prevent injury recurrence.