Background: Although exercise interventions are recommended in the management of subacromial pain syndrome (SPS), there is a lack of data regarding the exercises focusing on the principal biomechanical deficiencies that cause symptoms. Hypothesis: Utilizing progressive scapula retraction exercises (SRE) and glenohumeral rotation exercises (GRE) in the scapula stabilization program may lead to more reduction in symptoms and greater acromiohumeral distance (AHD) values. Study Design: A double-blind, randomized controlled trial. Level of Evidence: Level 2. Methods: A total of 33 patients were assigned randomly to either SRE or SRE+GRE. Both groups received a 12-week supervised rehabilitation program, including manual therapy and exercises (stretching and progressive scapula stabilization exercises). In addition, the SRE+GRE group performed GRE exercises at gradual elevation angles. From 12 to 24 weeks, patients performed exercise programs less frequently (3 times per week). Disability (shoulder pain and disability index [SPADI]), AHD (at 5 active abduction angles), pain intensity (visual analogue scale [VAS]), and patient satisfaction were recorded at baseline, 12 weeks, and 24 weeks. A total of 16 healthy individuals were recruited as a control group to compare AHD values. Data were analyzed using mixed model analyses of variance. Results: A statistically significant group-by-time interaction was found for AHD values ( F4,92 = 6.38; P = 0.001), a significant group-by-time interaction for SPADI-disability ( F1,33 = 5.148; P = 0.01), SPADI-total ( F1,32 = 4.172; P = 0.03), and for pain during activity ( F2,62 = 3.204; P = 0.05). However, no significant group-by-time interaction for SPADI-pain (F1,33 = 0.533; P = 0.48), for pain at rest (F1,31 < 0.001; P = 0.99), and at night (F1,32 = 2.166; P = 0.15). Yet, a significant time effect was observed. Conclusion: Progressive SRE and GRE in the scapula stabilization program lessens symptoms and improves AHD values in patients with SPS. Moreover, this program could preserve outcomes and further increase AHD when applied less frequently. Clinical Relevance: Utilizing SRE and GRE in the scapula stabilization program at gradual shoulder abduction angles provides better rehabilitation outcomes.