Introduction: Adolescence is an important phase of life with transition from school to college. Medical education in India is undergoing new changes with the introduction of a foundation course at the beginning of the MBBS course. We studied the effect of the foundation course among newly joined late adolescent medical students in improving their mental health. Methods: Volunteered students from two medical colleges took a pretest questionnaire consisting of their basic demographic details, and questions about their mental health, which was assessed using the Teenage Screening Questionnaire (TSQ)–Mental (Abridged) version by the Child Development Center (CDC), Trivandrum. A postfoundation course assessment on its role in reducing mental stress and improving awareness about medical education was collected from the students. Results: About 51.2% of the medical students were found to have increased stress in the past 1 month. The point prevalence of mental health illness in our study was 30.6%. The most common mental illness identified was anxiety (14.7%) and depression (14.7%) in an equal number of students. A small percentage of students (1.4%) had a severe form of depression with suicidal tendencies even before the start of the foundation course. Almost 76% of them opined that the foundation course had increased their fear and anxiety about present college life and future career. Conclusion: The foundation course has to be planned more meticulously with expert help, focusing more on the mental health aspect of the students, identifying best practices to improve the mental health of medical students who are at risk for mental illness in the future.