Medical students experience various stresses and many poor health behaviours. Previous studies consistently show that student wellbeing is at its lowest pre-exam. Little core-curriculum is traditionally dedicated to providing self-care skills for medical students. This paper describes the development, implementation and outcomes of the Health Enhancement Program (HEP) at Monash University. It comprises mindfulness and ESSENCE lifestyle programs, is experientially-based, and integrates with biomedical sciences, clinical skills and assessment. This study measured the program’s impact on medical student psychological distress and quality of life. A cohort study performed on the 2006 first-year intake measured effects of the HEP on various markers of wellbeing. Instruments used were the depression, anxiety and hostility subscales of the Symptom Checklist-90-R incorporating the Global Severity Index (GSI) and the WHO Quality of Life (WHOQOL) questionnaire. Pre-course data (T1) was gathered mid-semester and post-course data (T2) corresponded with pre-exam week. To examine differences between T1 and T2 repeated measures ANOVA was used for the GSI and two separate repeated measures MANOVAs were used to examine changes in the subscales of the SCL-90-R and the WHOQOL-BREF. Follow-up t-tests were conducted to examine differences between individual subscales. A total of 148 of an eligible 270 students returned data at T1 and T2 giving a response rate of 55%. 90.5% of students reported personally applying the mindfulness practices. Improved student wellbeing was noted on all measures and reached statistical significance for the depression (mean T1 = 0.91, T2 = 0.78; p = 0.01) and hostility (0.62, 0.49; 0.03) subscales and the GSI (0.73, 0.64; 0.02) of the SCL-90, but not the anxiety subscale (0.62, 0.54; 0.11). Statistically significant results were also found for the psychological domain (62.42, 65.62; p < 0.001) but not the physical domain (69.11, 70.90; p = 0.07) of the WHOQOL. This study is the first to demonstrate an overall improvement in medical student wellbeing during the pre-exam period suggesting that the common decline in wellbeing is avoidable. Although the findings of this study indicate the potential for improving student wellbeing at the same time as meeting important learning objectives, the limitations in study design due to the current duration of follow-up and lack of a control group means that the data should be interpreted with caution. Future research should be directed at determining the contribution of individual program components, long-term outcomes, and impacts on future attitudes and clinical practice.