Background: The shoulder complex is highly loaded during swimming. No studies were found analyzing the changes in shoulder girdle strength in young swimmers, through the years. Objective: To analyze the changes in strength of internal rotators and external rotators of the arm, lower trapezius and supraspinatus and in the external rotators/internal rotators ratio in young elite swimmers through 3 years. Methods: 31 adolescent elite swimmers (14–18 years, of both sexes) participated in the study. Isometric strength of the shoulder girdle muscles was performed using a handheld dynamometer during 3 years. Results: For boys absolute data, internal rotators increased from the first to the second (p = 0.0001; mean difference 45.6 N; 95%CI 26.7–65.0) and third years (p = 0.01; mean difference: 32.4; 95%CI: 9.3–55.5). Considering the weight-normalized data, internal rotators increased from the first to the second year (p < 0.0001; mean difference: 0.52; 95%CI: 0.26–0.78), external rotators decreased from the first to the third year (p = 0.003; mean difference: −0.33; 95%CI: −0.53 to −0.13) and from the second to the third year (p = 0.0004; mean difference: −0.29; 95%CI: −0.46 to −0.12) and supraspinatus decreased from the second to the third year (p = 0.006; mean difference: −0.17; 95%CI: −0.28 to −0.06). For girls, there were no significant differences in the absolute strength. Considering the weight-normalized data, lower trapezius decreased from the first to the third year (p = 0.02; mean difference: −0.15; 95%CI: −0.27 to 0.03). Considering both sexes, the external rotators/internal rotators ratio decreased from the first to the second (p < 0.0001; mean difference −0.12 N; 95%CI −0.13 to −0.11) and third years (p < 0.0001; mean difference −0.15 N; 95%CI −0.16 to −0.14). Conclusion: Muscle imbalance can occur in the shoulder girdle in young swimmers in 3 years, with increased internal rotators and decreased external rotators and supraspinatus strength in boys, and decreased strength of the lower trapezius in girls. Attention should be given in young swimmers’ shoulder girdle muscle balance.