Background: In February 2020, as coronavirus disease 2019 (COVID-19) spread rapidly in Daegu, South Korea, students in that region experienced many emotional difficulties. In this study, we analyzed the stress and emotional crisis experienced by students during the COVID-19 pandemic, its causative factors, and the factors that affect negative emotions. Methods: We identified the demographic information related to the experiences of unbearable stress and emotional crisis and their causal factors at three points in time: before the pandemic, during its peak, and at the time of the survey (2–3 months after the peak). In addition, we analyzed the factors related to depression and anxiety experienced by students during the COVID-19 pandemic. The Korean version of the Patient Health Questionnaire 9 and the Korean version of the Generalized Anxiety Disorder 7 was used to assess for depressive and anxiety symptoms in the subject students, respectively. Results: A total of 8,177 students participated in the analysis, with 4,072 boys (49.8%), 4,105 girls (50.2%), and 4,463 middle school students (54.6%) and 3,177 high school students (45.4%). The percentage of students who experienced unbearable stress was 9% before the COVID-19 pandemic, increased to 16% at the peak of the COVID-19 pandemic, then decreased to 12.7% at the time of the survey. Stress was experienced more by girls (18.1% versus 13.8% in boys; χ2 = 28.159, P < 0.001) and high school students (19.0% versus 13.5% in middle school students; χ2 = 45.437, P < 0.001). Overall, 7.6% experienced emotional crises during the COVID-19 pandemic, which was more prevalent in girls (10.1% versus 5.2% in boys; χ2 = 71.025, P < 0.001) and in high school students (8.8% versus 6.7% in middle school students; χ2 = 12.996, P < 0.001). Depression and anxiety was seen in 19.8% and 12.3% of students during the COVID-19 pandemic, respectively. The risk factors for depression and anxiety included unbearable stress before the COVID-19 pandemic (P < 0.001), mental health (P = 0.044), and age (P = 0.040), whereas resilience was identified as a protective factor for depression and anxiety (P = 0.001). Conclusion Students in Daegu experienced lots of mental difficulties since the COVID-19 pandemic. It will be necessary to improve stress management and resilience to improve students' mental health in disasters such as the COVID-19 pandemic.