Background:The perceived stress and anxiety among medical students have bleak consequences on their academic performances, physical, and psychological wellbeing. However, there is a dearth of reliable epidemiological studies in Ethiopia on medical student's experience of stress and anxiety. Therefore, this study was aimed to determine the prevalence and identify factors associated with stress and anxiety among undergraduate medical students of Haramaya University, Eastern Ethiopia. Methods: An institutional-based cross-sectional study was conducted from May 13 to June 12, 2019 among 523 participants selected by simple random sampling technique. Data were collected by using structured questionarie through self-adminstered method. Data were entered by Epidata version 3.1 and analyzed using Stastical Package for Social Science(SPSS) version 22. Bivariableand multivariable logistic regression analysis were conducted to identify factors associated with anxiety and stress. Adjusted Odd Ratio (AOR) and 95% Confidence Interval(CI) was used to show the strength of association, and P-value of 0.05 was used to declare statistical significance. Results: The prevalence of stress was 44% (95% CI: 40.2%-48.2%) and anxiety was 48.9% (95% CI: 44.6%−53.3%) among undergraduate medical students of Haramaya University. Being female (AOR=1.90, 95% CI: 1.28-2.81) and living off-campus (AOR=1.75, 95% CI: 1.12-2.73) were factors significantly associated with both stress and anxiety. Whereas, alcohol use (AOR=2.26, 95% CI: 1.50-3.50) and smoking cigarette (AOR=3.50, 95% CI: 1.58-7.73) linked with stress. The poor psychosocial support (AOR=1.93, 95% CI: 1.20-3.20) was significantly associated with anxiety. Conclusion: Substantially a higher level of stress and anxiety was reported. Being female and living off-campus were linked with both stress and anxiety. Where as, alcohol use and smoking cigarette were associated with stress and poor psychological support was significantly associated with anxiety.