Chronic ankle instability (CAI) has a higher frequency in soccer due to the rapid changes in body movement. Thus, this study compared the effects of eight weeks of a hopping protocol and a combined protocol of balance plus strength in a within-between group analysis. Thirty-six male professional soccer players participated in this study and were randomly allocated in three groups: control group (CG, n = 12), hopping group (HG, n = 12), and balance plus strength group (BSG, n = 12). Strength, static and dynamic balance, and function were assessed at baseline and eight weeks post intervention. First, Foot and Ankle Ability Measure (FAAM) and FAAM sport scales were applied. Then, a dynamometer was used to measure strength of the muscles around the hip, knee, and ankle joints. The Bass stick measured static balance and the Y balance test measured dynamic balance. Additionally, functional tests were carried out by Triple Hop, the Figure 8 hop, and vertical jump. A repeated measures ANOVA [(3 groups) × 2 moments] was used to compare the within and between group differences. In general, all tests improved after eight weeks of training with both protocols. Specifically, the BSG improved with large ES for all tests, while the HG improved all test with small to large effect sizes (ES). Furthermore, HG showed higher values for vertical jump (p < 0.01, ES = 1.88) and FAAMSPORT (p < 0.05, ES = 0.15) than BSG. BSG showed higher values for hip abduction (p < 0.05, ES = 2.77), hip adduction (p < 0.05, ES = 0.87), and ankle inversion (p < 0.001, ES = 1.50) strength tests, while HG showed higher values for knee flexion [ES = 0.86, (0.02, 1.69)] and ankle plantarflexion [ES = 0.52, (−0.29, 1.33)]. Balance plus strength protocol showed more positive effects than the hopping protocol alone for soccer players with CAI.