(1) Background: Mental well-being and mental health problems are both important, especially among medical students who will be future doctors. The proposed study aimed to explore both positive and negative mental health experiences, especially mistreatment, occurring among medical students in their clinical years. (2) Methods/design: The study will conduct a cross-sectional survey between January 2021 and December 2021, among medical students studying in their clinical years across 23 medical schools throughout Thailand. Measurements regarding character strengths related to medical professionalism as well as other positive mental health strengths and negative mental health problems, e.g., anxiety, depression and experience of mistreatment will be completed. Both medical students and faculty members will be invited to participate in the study. (3) Discussion: this survey will provide an overall picture of medical students’ mental well-being, positive and negative aspects of mental health and the magnitude of mistreatment and perspectives they experience. The limitations of the survey will be discussed.