Background and Objectives: This study aimed to examine the development of clinical competence of novice physical therapists (PTs) during their first year of employment, following the implementation of an original in-house educational program. The educational program was designed to offer diverse training opportunities at an early stage, during the first year of employment. Methods: Thirty-eight novice PTs (21 males and 17 females, mean age 23.4 ± 3.2 years) participated in this study. All participants underwent educational programs and a self-assessment using the Clinical Competence Evaluation Scale in Physical Therapy (CEPT) on the first day of employment (entry-level) and after 1, 3, 6, and 12 months of employment. The total score and CEPT component-wise scores—“knowledge,” “clinical reasoning,” “skill,” “communication,” “attitude,” “self-education,” and “self-management”—at the 4 assessment points (1, 3, 6, and 12 months) were compared with values on the first day. Results: The total scores at 3, 6, and 12 months of employment were significantly higher than those on the first day of employment (P < .05). Among the total scores on the 7 components, those for “knowledge,” “clinical reasoning,” “skill,” and “communication” at 3, 6, and 12 months after employment were also significantly higher than those on the first day of employment (P < .05). The scores for “attitude” and “self-education” 12 months after employment were significantly higher than those on the first day of employment. However, the “self-management” scores at 1, 3, 6, and 12 months after employment did not significantly change compared with those on the first day of employment. Conclusions: The total score was significantly higher after 3 months. The participant’s clinical competence may have improved because they participated in an educational program related to “knowledge,” “clinical reasoning,” “skills,” and “communication” at an earlier stage in the first year. However, their progress was comparatively slower in other areas, suggesting that the content might not have been sufficient. This study revealed the effectiveness of the educational program on novice PTs’ clinical competence at a single institution in Japan. Positive outcomes were obtained for several parameters. Furthermore, the results reveal the need for content modifications within the educational program to improve PTs’ performance across all evaluated items.