BACKGROUND: Self-regulated learning (SRL) is a critical skill for medical students to reach their learning goals in the bedside clinical rotations. This study was performed with the aim of comparing SRL and motivation of 4th year medical students who are in their educational transition between students with mentors and those without mentors. MATERIALS AND METHODS: This study was cross-sectional. A total of 196 medical students were invited to complete a form consisting the motivation and SRL questionnaire through Google form during their 1st year of clinical clerkship, while some of them had participated in the mentoring program beforehand. data correlation and regression analysis were employed. RESULTS: Comparing SRL and motivational beliefs scores between students with mentors and without mentors indicated that motivational beliefs mean score in students with mentors (87.5 ± 8.44) was significantly higher compared to the others (83.49 ± 7.36) (P = 0.005). Among SRL subscales, planning and examination stress were significantly different between two groups with higher scores for mentees (P = 0.033 and 0.021). Having a mentor predicted motivational beliefs with OR = 7.974 (1.391–45.719) and P = 0.020. CONCLUSION: Considering a significant correlation between mentor possession and the scale of motivation beliefs, future longitudinal and interventional research besides the customized mentoring program is required to understand the role of mentoring programs on SRL as a cause-and-effect relationship to recommend the peer mentoring program to enhance SRL skills in the medical students especially during their transition to the new clinical environment.