© 2019 Kelly et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Background In response to a physician shortage in Ethiopia, the number of medical students admitted to public universities was rapidly increased through a “flooding” policy. Objectives To assess medical student perceptions on the impact of the “flooding” policy on medical education and e-learning initiatives, as well as plans for future emigration. Design A cross-sectional survey of medical students at AAU was implemented in 2014. Attitude and practice items were assessed using a Likert scale. Logistic regression analysis was performed to identify characteristics associated with an interest in future emigration. Results 673 (99.6%) of 676 students approached completed the survey, representing 39.5% of all 1705 medical students enrolled at AAU in 2014. Most students felt the “flooding” policy had a negative impact on their medical education and >90% felt there was not adequate infrastructure to support the increased student body. E-learning activities to accommodate increased class size included distribution of electronic tablets, but at the time of the survey only 34.8% of students still had a working tablet and 82.3% reported problems with internet connectivity. Most preclinical students (85.1%) who had attended live-streamed lectures preferred traditional classroom lectures. Half of the students (49.5%) intended to practice medicine in Ethiopia. Independent risk factors for planning to emigrate included age <21 years (aOR = 1.30, 95% CI 1.04, 1.97); having applied to medical school for reasons other than “wanting to be a physician” (aOR = 1.55, 95% CI 1.14, 2.20), and not believing that “flooding” policy would increase the number of physicians working in Ethiopia (aOR = 1.87, 95% CI 1.33, 2.58). Conclusions The “flooding” policy lead to significant educational challenges that were not fully alleviated by e-learning initiatives. Concomitant increases in resources for infrastructure development and faculty expansion are needed to maintain quality medical education. Additional research is needed on factors that influence medical graduates decision to emigrate.