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Background: The residency program as a part of the clinical services itself has been influenced by the COVID-19 outbreak. Several reports have been published regarding the impact of COVID-19 on the residency programs; however, all studies were performed in developed countries or did not comprehensively analyze what residents think about the COVID-19 impact on their residency program. We investigated the impact of the COVID-19 pandemic on the pediatric surgery residency program in our institution as an important part of hospital medical services. Methods: We developed and distributed a questionnaire to pediatric surgery residents in our institution who were registered from January 2015–July 2020. The questionnaire was consisting of 24 questions: a) the perspectives of residents about COVID-19 infection during their residency program; b) the learning process; c) academic evaluations; and d) residents' suggestions to improve the quality of their residency program during the outbreak. Results: Most (82.6%) pediatric surgery residents agreed that elective surgeries should be postponed during the pandemic. Before the outbreak, almost all (82.6%) residents used textbooks and journals as their primary sources of learning, while during the outbreak, 69.5% of residents shifted to use online lectures either from the school or Association of Pediatric Surgeons. Interestingly, 91.3% of participants agreed that they had more time to complete their academic assignments during the pandemic. Conclusions: The pandemic has had a significant impact on the development of pediatric surgery residency programs. Moreover, the responses to the questionnaire are affected by the seniority and sex of the residents. A comprehensive approach is needed to maintain the high standard of competence of pediatric surgery without compromising our safety from the COVID-19 infection risk.