Background: Physiological responses to stress disturb internal homeostasis, leading to serious health consequences. Medical students experience high stress levels that should be managed promptly to prevent stress-related impacts on students’ health and education. Aim: This study aims to identify the relationship between stress factors, general health, and academic performance. Methods: This study recruited 421 medical students of all academic years. Participants completed an online survey assessing stress levels using a validated 10-item Perceived Stress Scale. Stress was also compared with students’ health and academic performance. Results: We found that 93.6% of our sample experienced moderate to severe stress, and 31% reported increased stress due to the coronavirus disease (COVID-19) pandemic. Except for internship students, stress significantly decreases as students progress each academic year (p < 0.05). Students with higher GPAs and with comorbidities are more stressed. Comorbidities were primarily reported in students in their final years of education with a 4% lower GPA than healthy students. Although we had three stress-related themes (general, academic, and pandemic), students’ perceptions of stress factors were primarily academically related. Conclusions: Students experience high stress levels in their final educational years, which might increase the risk of health issues and low academic performance. It is essential to innovate stress-coping strategies specially designed for medical students and mandatorily provided by all medical colleges and to educate students on the effects of stress on their health.