The study determined the presence of theory-practice gap in physical therapy education in the Philippines from the perspectives of three different groups: interns, clinical instructors, and internship coordinators. It utilized both quantitative and qualitative research designs using survey, interviews and focus group discussions in collecting data. The Clinical Internship Evaluation Tool was used as the primary data gathering instrument to measure the actual competencies of the interns. A survey questionnaire and interview guide was used to ascertain perceptions of the stakeholders on the clinical education process. Focus group discussions and interviews were audiotaped, and verbatim transcripts were produced. Descriptive statistics and t-test was used for data analysis. The result of t test revealed that the interns’ actual competencies are significantly different from the standards of competence expected of a competent clinician. Moreover, identified as the most problematic professional behavior and patient management skills were initiative and patient evaluation, respectively. Further, there were a pronounced gap between what they learned in school and what they are expected to do at the clinical sites. The highlighted gaps can contribute to quality appraisal, conformance to standards and enrichment of physical therapy education. Schools must facilitate better teaching-learning by more didactic instruction, laboratory skill mastery, and modification of academic contents. Clinical instructors in affiliation centers should have adequate education and preparation for their supervisory and teaching roles to enhance the clinical education process effectively.