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Abstract Background Causal mediation analysis is one way to bridge this gap by exploring the causal pathways of a given intervention. The aim of this study was to assess whether scapular motion, position, and periscapular muscle strength are mediators for pain and shoulder disability outcomes following a scapular stabilization intervention for patients with subacromial pain syndrome. Methods Sixty patients were randomized into two groups: scapular stabilization or periscapular strengthening exercises. The intervention consisted of three sessions per week for 8 weeks. The primary outcome measures were pain and disability and the following outcome measures were considered as potential mediators: scapular motion, scapular position, periscapular muscle strength, age, duration of symptoms, and side of the complaint. A model-based inference approach with bootstrap simulations was used to estimate the average causal mediation effect, average direct effect, and the average total effect from the data of a randomized clinical trial that evaluated the effect of adding scapular stabilization exercises to a scapulothoracic strengthening program in people with subacromial pain syndrome. Results The results demonstrated that none of the putative mediators were influenced by the intervention. However, muscle strength of serratus anterior, upper, middle, and lower trapezius muscles was associated with shoulder disability. Conclusion Scapular kinematic and periscapular muscle strength did not mediate the effect of scapular stabilization exercises on shoulder pain or disability scores in subjects with subacromial pain syndrome. Muscle strength of serratus anterior, upper, middle and lower trapezius were associated with shoulder disability scores at 8-weeks follow-up.