Introduction: The coronavirus disease 2019 (COVID-19) has negatively impacted healthcare services worldwide. We hypothesized that the pandemic would affect our case mix and mortality. Our objective was to study this impact. Methods: We retrospectively studied all patients who underwent congenital heart surgeries from March 21st to August 21st in 2019 and 2020 using the institutional electronic database. We compared demographic data, preoperative and postoperative length of stay (LOS), risk stratification using Risk Adjustment for Congenital Heart Surgery (RACHS) classification and outcomes in both periods. Results: We observed a 66.7% decrease in our surgical volume (285 × 95 patients). Patients operated in the pre-pandemic period were older (911.3 174.8 - 5953.8 days-old) compared to the pandemic period (275 days-old; P<0.05). When the case mix was compared between periods, the percentage of neonatal surgery was increased in the pandemic era (8% × 21.1%; P<0.05), and the number of RACHS 1-2 surgeries decreased significantly (60.7 × 27.4%; P<0.05). Preoperative LOS was increased in the pandemic period (1.2 × 7 days; P=0.001). There was no significant increment in mortality (P=0.1). Two patients tested positive for COVID-19 in the postoperative period and both died. Conclusion: Our program observed a sudden decrease in surgical volume and a consequent increase in surgical complexity. There was a non-significant increment in mortality.