Background: The COVID-19 pandemic had a significant impact on the population’s ability to be physically active. Purpose: Evaluate the effect of the COVID-19 mitigation measures on exercise tolerance in patients with congenital heart disease (CHD). Materials and methods: All subjects (880, 6–18 years old) who performed a stress test at our hospital from October 2020 to February 2021 and had a similar test one year earlier were enrolled. A questionnaire on the degree of physical activity carried out in 2020 concerning the period prior to the pandemic was compiled. Exercise tolerance and the main anthropometric parameters between the first and second tests were compared. Results: 110 subjects (11.9 ± 4.1 years) were included in the study. The percentage of patients engaged in regular physical activity (RPA) decreased significantly during the pandemic (p < 0.001), and BMI increased significantly (p < 0.001), except among the subjects who began RPA during the lockdown, whereas test duration did not decrease significantly overall but increased in this last subgroup (p < 0.05) Conclusions: The COVID-19 lockdown led to a less active lifestyle with a significant increase in BMI in our group of CHD. These data could have negative effects on the risk profile of this population. RPA practiced at home seems to be effective in counteracting such effects.