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Abstract Background The rigors of medical education often take a toll on students' mental well-being, resulting in heightened stress, anxiety, depression, somatization, and thoughts of self-harm. This study aimed to determine the prevalence of mental health problems among Jordanian medical students (Yarmouk University), explore the links between mental state and demographic and lifestyle factors, and compare mental health profiles between pre-clinical/pre-clerkship (years 1–3) and clinical/clerkship (years 4–6) students. Methods An online survey was distributed to undergraduate medical students at Yarmouk University. Mental health was measured using validated tools (depression: Patient Health Questionnaire, PHQ-9; eating disorders: SCOFF; Generalized Anxiety Disorder Scale, GAD-7; Somatic Symptoms: Patient Health Questionnaire, PHQ-15; overall stress (single-item measure); ability to handle stress; stressors and coping mechanisms. Data on sociodemographic factors, academic performance, and lifestyle choices, also were collected. Bivariate and multivariable analyses evaluated the associations between academic level and mental health, accounting for sociodemographic and lifestyle factors. Results Of the 618 medical students who responded, 48.4% screened positive for depression, 36.7% for anxiety, and 63.6% for high level of stress. Slightly over half experienced somatic symptoms, and 28.6% exhibited signs of eating disorders. Roughly, 26% had suicidal thoughts, as measured by item 9 of the PHQ-9 scale. Low reported rates of healthy behaviors were observed (e.g. balanced diets, 5.7%; vigorous physical activity, 17.0%). Smoking prevalence was 24.6%, notably higher among clinical students. At the multivariable level, stress, insomnia, eating disorders and cigarette smoking were significantly associated with depression, anxiety and somatization. Higher physical activity scores were associated with lower depression risk. Females were significantly more likely than males to fall in more severe somatization categories. Conclusion This study highlights the need to address the alarming rates of mental health problems among Jordanian medical students. While few significant differences were observed between pre-clinical and clinical students, the high rates of depression, anxiety, stress, and negative health practices in both groups suggest the need for interventions that begin at enrollment as well as during transitions to clinical settings. Prioritizing mental health support and promoting healthier lifestyles among medical students are vital steps toward nurturing resilient, well-rounded future medical professionals.