Introduction Clinical reasoning (CR) is a core clinical skill that has been directly linked with patient outcomes. Therefore, developing sound clinical reasoning skills in students should be a concern for physical therapy (PT) professional education programs. Purpose To develop an understanding of PT student perceptions of CR and how they best learn it to inform future educational practice and research needs. Method A systematic review of the literature was conducted using the databases PubMed, CINAHL, ERIC, and Cochrane database of systematic reviews to develop an understanding of how students perceive CR throughout their professional education programs and how they best learn it. Results Fifteen articles met inclusion criteria. Three major themes were identified from the systematic review. First, student perceptions of CR changes throughout their professional education programs from therapist-centric to client-centered. Second, students prefer educational experiences that mirror anticipated real-world experiences like case-method teaching. Lastly, educational experiences designed to enhance CR capability enhances student professional formation and identity. Discussion Recent calls for reform across all levels of physical therapy education has been made. In part, these reform efforts emphasize the need for PT education programs to provide learner-centered education through practice-based learning experiences and developing adaptive learners. The results of the systematic review support these aims. More research is needed regarding the impact of educational experiences on student CR skill development as well as more valid and reliable tools for assessing CR capability in PT students.