Introduction: Stress, anxiety, and depression are common psychological health concerns among university students worldwide, often impairing academic performance, relationships, and overall well-being. In Mongolia, limited research has addressed these issues. This study aimed to assess the prevalence of stress, anxiety, and depression among students at the Mongolian University of Pharmaceutical Sciences (MUPS) using the Depression, Anxiety, and Stress Scale (DASS-21) and to identify associated factors. Methods: A cross-sectional survey was conducted with 214 students aged 18–50 years. Data were collected through the DASS-21 and analyzed using SPSS. Descriptive statistics determined prevalence, while inferential analyses explored associations between mental health outcomes and sociodemographic or contextual variables. Results: Mental health challenges were highly prevalent among MUPS students. Nearly one-third of those aged 18–25 reported high or extremely high stress, while older students (36–50 years) showed elevated depression and anxiety levels. First-, fifth-, and sixth-year students were particularly vulnerable, with almost half experiencing very high stress or anxiety. Pharmaceutical students reported higher rates of depression and stress, whereas traditional medicine students reported more stress and anxiety. Environmental conditions (p=0.020), health status (p=0.001), financial difficulties (p=0.037), and interpersonal relationship problems (p=0.023) were significantly associated with adverse outcomes. Conclusion The findings highlight the urgent need for targeted interventions to reduce stress, anxiety, and depression among MUPS students. Policies and preventive strategies addressing environmental, health related, financial, and social factors are essential to promote student well-being.