Objective To compare the efficacy and underlying mechanisms of scapular dyskinesis-based exercise therapy (SDBET) and multimodal physical therapy (MPT) in young male overhead athletes with subacromial impingement syndrome (SIS) and scapular dyskinesis (SD). Methods This single-center, single-blind, parallel-group superiority randomized controlled trial was designed to compare two interventions in athletes clinically diagnosed with SIS and SD. Outcome assessors were blinded to group allocation. Sample size was determined a priori using G*Power (f = 0.25, alpha = 0.05, power = 0.80), yielding a required sample of 28; 32 participants were planned to account for potential dropout. Inclusion criteria were: male overhead athletes aged 18-25 years with clinically diagnosed SIS and SD. Exclusion criteria included prior surgery or other contraindications. Participants were randomized to either SDBET or MPT groups. Both groups received 8 weeks of intervention (3 sessions/week) and a 4-week follow-up. The primary variable was disability, measured using the Shoulder Pain and Disability Index (SPADI). The secondary variables were pain (measured using the Visual Analog Scale [VAS]), shoulder active range of motion (AROM, measured using goniometry), strength (measured using Isometric Strength Tests [IST] of scapular stabilizers and external rotators), and scapular kinematics (measured using the Scapular Dyskinesis Test [SDT]). Assessments were conducted at baseline, week 8, and week 12. Result A total of 32 participants were analyzed (SDBET group: n = 16; MPT group: n = 16). Mixed-design ANOVA revealed significant main effects of time for all outcomes (all p < 0.001, eta(2) = 0.71-0.92), and significant group effects for SPADI and IST (p < 0.01). Significant Time x Group interactions were also observed for all variables (p < 0.05, eta(2) = 0.15-0.76), prompting further simple effects analysis. Disability (SPADI) decreased significantly in both groups by week 8 (p < 0.001, eta(2) = 0.03), with no between-group difference. However, only the SDBET group maintained improvements at week 12 (p < 0.001, eta(2) = 0.59). Pain (VAS) decreased more in the MPT group at week 8 (p = 0.018, eta(2) = 0.17), but rebounded by week 12, eliminating group differences (p = 0.268, eta(2) = 0.04). Active range of motion (AROM) improved in both groups by week 8 (p < 0.001), with only the SDBET group sustaining these gains at week 12 (p < 0.001, eta(2) = 0.37). Strength (IST of scapular stabilizers and external rotators) improved exclusively in the SDBET group at both week 8 and 12 (all p < 0.001), with significant between-group differences (eta(2) = 0.57-0.74). Scapular kinematics (SDT) improved in 43.8% of SDBET participants, while no change was observed in the MPT group (p = 0.001-0.004). Conclusion Both SDBET and MPT improved shoulder disability, pain and AROM in SIS patients with SD, but only SDBET showed lasting effects. Targeted therapy has more comprehensive and sustained effects.