The influx of Syrian refugees to Lebanon that began in 2012 created new health-care and financial stressors on the country with an increase in communicable and non-communicable diseases. This study aims to describe the presentations, diagnoses, management, financial burden, and outcomes among Syrian refugees with congenital heart disease (CHD) in Lebanon. This is a retrospective study that was conducted through reviewing the charts of all Syrian pediatric patients referred to the Children’s Heart Center at the American University of Beirut Medical Center for evaluation between the years 2012 and 2017. We reviewed the charts of 439 patients. The mean age at presentation was 3.97 years, and 205 patients (46.7%) were females. 99 Patients (22.6%) were found to have no heart disease, 69 (15.7%) had simple, 146 (33.3%) had moderate, and 125 (28.5%) had complex heart diseases. 176 (40.1%) Patients underwent interventional procedures, with a surgical mortality rate of 10.1%, compared to a rate of 2.9% among non-Syrian children. The average cost per surgical procedure was $15,160. CHD poses a significant health and financial burden on the Syrian refugee population in Lebanon, a small country with very limited resources. The Syrian cohort had a higher frequency of complex cardiac lesions, presented late with additional comorbidities, and had a strikingly elevated surgical mortality rate. Securing appropriate funds can improve the lives of this population, ease the financial burden on the hosting country, provide adequate health-care services, and improve morbidity and mortality.