Background Burnout, defined as mental and physical exhaustion, has been an issue for many medical students. Medical student burnout is associated with many factors such as academic pressure, sleep deprivation, exposure to patient suffering, and high academic demand. In this study, we assessed the prevalence of burnout symptoms among preclinical and clinical medical students studying at Qassim University in Qassim, Saudi Arabia. Results Three hundred thirty-six subjects entered the final data analysis with a majority between 18 and 24 years of age, of whom 56.5% was females and 43.5% was males. The overall burnout prevalence was 8%. The female gender was a significant predictor of emotional exhaustion and personal efficacy, (OR = 2.510; 95% Cl [1.845–3.415]; p value 0.000) and (OR = 1.434; 95% Cl [1.086–1.866]; p value 0.010), respectively. Conclusion Among medical students, burnout is common. The impact of gender on burnout was noticed; female gender was a significant predictor of emotional exhaustion and personal efficacy. Medical education style had no impact on burnout levels among medical students.