Purpose: This study was designed to develop an evaluation tool for assessing professional behavior and clinical competencies from the graduates’ perspective. Methods: This study employed mixed method in a sequential exploratory design. The semi-structured interviews were conducted with three graduates from different cohorts. The qualitative analysis of the interviews found six emerging themes for professional behavior and clinical competencies development. These themes were then developed into a 55-item questionnaire. The questionnaire was then distributed to 84 medical graduates for exploratory factor analysis (EFA) from February to April 2019. The quantitative data were analyzed using IBM SPSS ver. 21.0 (IBM Corp., Armonk, USA) for principal axis factoring. After conducting EFA, we proceeded with confirmatory factor analysis (CFA) with another 120 graduates to validate the tool. Results: Eighty-four graduates completed the questionnaire for EFA. Upon completion of EFA, 35 out of 55 items of the questionnaire were found to be valid and reliable. The most appropriate fit was seven factors, which explained 58.18% of variance between them after 15 iterations with Cronbach’s α of 0.916. The personal satisfaction factor was noted to be weak. It was therefore added to patient management factor due to its similar intention. The final EFA factor after the modification was six. The CFA found that 34 out of 35 items was valid and reliable that representation of the latent variables. Conclusion The questionnaire has achieved the desired construct validity score and can be used as an evaluation tool to assess professional behavior and clinical competencies from the graduates’ perspective.