Background Psychological disorders have negative consequences on students’ learning and academic performance. In addition, academic burnout is one of the common challenges that affects students’ motivation and academic eagerness; however, the determinant is not clear. Medical students, meanwhile, demand special attention due to their professional responsibilities. In this regard, this study is conducted to investigate the academic burnout, rate of depression, anxiety and stress as well as related factors among undergraduate medical students at the Tehran Medical Sciences Islamic Azad University. Methods This cross-sectional and descriptive study was performed on medical students of Islamic Azad University of Tehran in 2017. In phase I, conducted on all stager students, Maslach Burnout questionnaire was used. In phase II, the DASS-42 questionnaire was provided for 123 students, 120 of whom met the inclusion criteria. In addition, another questionnaire including gender, age, lifestyle, marital and financial status, nutrition style, vitamin D deficiency, smoking, study hours per week, work efficiency and distance from the place of residence to the teaching hospital was used. Finally, the data extracted by SPSS version 23 was analyzed at the significance level of 0.05. Results In phase I of the study, 17 subjects showed academic burnout (16.3%). Out of all, 76.5% of students with academic burnout did not focus on the study and students’ academic burnout was associated with a decrease in their focus (P < 0.05). However, the relationship between academic burnout and other factors was not significant. In phase II, the prevalence of depression, anxiety and stress was 37.5, 41.1 and 30.3%, respectively. The prevalence of severe and very severe degrees that required psychiatric follow-up were 10.5, 10.5 and 7% for depression, anxiety and stress, respectively. According to statistical analyzes, there is a significant direct relationship between anxiety and the distance from the place of residence to the teaching hospital (P = 0.040). Conclusion The present study estimated the prevalence of academic burnout to be between 9.2 and 23.4%, considering the 5% error in the calculation, and the level of anxiety was related to the distance from the place of residence to the hospital.