The COVID-19 pandemic has led to substantial modifications in the undergraduate medical curriculum, with numerous in-person clinical sessions being replaced by online teaching methods. This study seeks to examine the relationship between medical students’ stress levels during the pandemic and their performance in the final examinations. This cross-sectional study utilized a questionnaire-based approach to assess students’ stress levels, measured using the COVID-19 Student Stress Questionnaire (CSSQ). The relationship between stress levels and students’ performance in the final examinations was subsequently analyzed. A total of 110 out of 221 (49.8%) final-year medical students completed the questionnaire. Among them, 13 students failed the final examination (cases), while 97 students passed (controls). Baseline demographic characteristics were comparable between cases and controls, with a median age of 24 years in both groups. Cases reported higher stress levels across all domains, including concerns related to risk of infection, social isolation, relationships with family, peers, and faculty, academic life, and sexual life, compared to controls. Notably, academic-related stress was significantly greater among cases than controls (p < 0.01); all cases (100%) described their academic experience during the COVID-19 pandemic as “very” or “extremely” stressful, in contrast to 35.1% of controls. Elevated stress related to academics and studying during the COVID-19 pandemic was associated with poorer performance in the final examination. These findings highlight the need for enhanced academic support to address students’ needs during such disruptive periods.