Introduction The sudden shutdown caused by coronavirus disease 2019 has far-reaching effects, including on education and training. For this reason, traditional education and training have shifted to an online learning format. This study explores the challenges of and barriers to e-learning experienced by trainers and training coordinators in the Saudi Ministry of Health during the coronavirus disease 2019 pandemic. Methods A cross sectional survey was distributed among participants by email. The sample included 262 trainers and training coordinators currently working for the Saudi Ministry of Health in hospitals, primary health care centers, and training centers (including general directorates of regions and clusters) in all 13 administrative regions of the country. Results Most participants exhibited an intermediate level of experience with e-learning (58.4%) and found the task of adapting to unfamiliar technology to be a challenge (22.1%). Limited social interaction in relation to cheating/plagiarism contexts, frequent technological failures, and a lack of policies or standards for e-learning were significant barriers for participants; these were mentioned by 46.9%, 43.5%, and 40.1% of participants, respectively. Conclusions This study highlights the challenges and barriers encountered in the adoption of e-learning by trainers and training coordinators in the Saudi Ministry of Health. The challenges of and barriers to e-learning included but were not limited to communication, assessment of trainees, adaptation to a lack of policy, and frequent technology failure. Adapting to new technologies is challenging for trainers and training coordinators, which is exacerbated by a lack of adequate policies and standards to eliminate cheating and avoid technological failures. These results could help bridge gaps in the use of e-learning by improving policies, holding workshops and training sessions, and providing continuous information technology support in e-learning.