Background and objectives The novel coronavirus disease 2019 (COVID-19) pandemic has challenged healthcare systems worldwide. Various studies have revealed the negative impact of the pandemic on the education and mental health of medical students and residents. In this study, we aimed to explore the effects of the COVID-19 pandemic on medical interns' educational experience, clinical practice, and mental health. We also engage in a discussion on the compensatory methods that have been adopted to improve medical interns' learning processes during the ongoing pandemic. Methods This cross-sectional survey-based study was conducted at the King Saud University Medical City (KSUMC) in Riyadh, Kingdom of Saudi Arabia (KSA) from March to October 2020. The participants consisted of medical interns. The survey collected information on participants' demographics, training, and the educational and psychological impact of the pandemic. Results The survey was distributed to 480 medical interns, of whom 345 (71.8%) participated. Most of our sample (75.6%) believed that the COVID-19 pandemic has negatively impacted their cumulative experience. Regarding the pandemic's impact on training and education, it was found that the emergency department rotation was the most affected rotation (60.3%). The majority of the participants (55.9%) believed that all tracks have received equal education and the volume of patients seen by interns decreased by 91.9%. As for the compensatory methods, 73.3% reported the utilization of remote platforms. Regarding the pandemic's mental health impact, 36% believed that it has affected their mental health, where increased stress levels were noticed in 47.8% of participants. Statistical significance was found in both Patient Health Questionnaire-9 (PHQ-9) and General Anxiety Disorder-7 (GAD-7) scores, which indicated that during the pandemic, 20.6% of the participants suffered from depression, and 13.9% had moderate to severe anxiety. Conclusions This study highlights the negative educational and psychological impact of COVID-19 on medical interns. With emerging infectious diseases on the rise, recognizing the impact of COVID-19 on medical interns is vital to improving interns' educational experiences and mental health during future crises.