Athletes are susceptible to acute as well as chronic shoulder injury, compromising their ability to fully compete. This chapter describes science-based guidelines for shoulder rehabilitation following both microtraumatic and macrotraumatic events that commonly affect athletes. This chapter outlines clinical interventions, focusing on rotator cuff exercises, scapular muscle training, and implementation of kinetic chain variables into functional exercises in sport-specific conditions. This chapter describes a phased and criteria-based approach with milestones to progress culminating in clinical return-to-play criteria.