Purpose The COVID-19 pandemic has limited the traditional way of teaching due to contact restrictions and the trainees being the front-line providers of patient care in certain specialties. During the pandemic, many academic institutes have adopted various methods for utilizing online learning as an alternative to traditional teaching. Numerous studies reported the impact of these changes on medical education with varying results. As such, comprehensive assessments are necessary to evaluate the outcomes of this rapid transformation. The aim of this study was to provide qualitative and quantitative assessments of post-graduate online medical education during the COVID-19 pandemic in Saudi Arabia. Participants and Methods In this cross-sectional study, an online questionnaire was distributed among postgraduate trainers and trainees in Riyadh second health cluster. The questionnaire was used to assess the experiences, perception, coping, satisfaction and preferences of medical trainers and trainees towards online education during the COVID-19 pandemic. Results A total of 207 participants were involved in this study. While the sociodemographics differed between trainers and trainees, age was significantly associated with negative pre-pandemic online learning experiences. Stress was reported among both groups and was significantly correlated with the pre-pandemic computer and internet competency. Coping was reported to be easier by trainers compared to trainees. The overall perception of online learning was positive in 73% of the respondents. Perception significantly correlated with age, stress, coping and satisfaction (P < 0.0001). The majority of trainees were interested in a hybrid mode learning, combining traditional teaching with online education. Conclusion There is a significant difference between trainers and trainees with regard to their experience of online education. Further studies are required to assess how to effectively implement online education in postgraduate training programs and identify strategies to overcome the reported deficiencies.