The new coronavirus infection, which was first seen in China in late December, 2019 and eventually became a worldwide pandemic, poses a serious threat to public health. After a high spike in the number of new COVID-19 infection cases following the increase in overall daily death toll in Turkey, Turkish Ministry of Health has taken immediate precautions to postpone elective surgeries in order to reduce the burden to the healthcare system which might be challenged. Whereas different areas of medicine were able to suspend their operative procedures during this period, this was not completely possible in paediatric cardiovascular surgery due to the severity and urgency of congenital heart disease patients requiring operation. Based on the guideline that was published by the Turkish Paediatric Cardiology and Cardiac Surgery Association, in which the patients requiring surgical intervention during the COVID-19 pandemic period are ranked according to the priority, directions were given regarding the operations that hereby, be delayed, we report our experience in 29 cases retrospectively, regarding the pre-operative evaluation of these patients, makings of an emergency operation decision, and strategies taken about intra-operative and post-operative management and arrangements during the pandemic period. In this article, we present crucial precautions that were applied in paediatric cardiovascular surgery and extensive list of cases in order to deliver highest level of the patient safety and protection for the surgical team.