Background Cardiac magnetic resonance imaging (MRI) is an important diagnostic tool for congenital heart disease (CHD), as reflected by class 1 recommendations for the use of cardiac MRI by various consensus panels. However, little is known about the safety and clinical utility of cardiac MRI for these critically ill infants with CHD, whose further management cannot be directed by echocardiography. This study aimed to assess the safety, the potential hemodynamic side effects, and the clinical benefits of cardiac MRI for infants with complex CHD during their intensive care unit stay. Methods Infants referred from the pediatric cardiac intensive care unit (PCICU) to the authors’ cardiac MRI program in the past 2 years were retrospectively analyzed using the electronic chart system available at their institution. Data collected included age, diagnosis, inotropic support, urine output, diuretic medication, body temperature and lactate levels, length of MRI examination, adverse effects during and after the procedure, clinical implications of MRI, length of stay in the PCICU, and mean blood pressure and heart rate before, during, and after MRI. Results Among 592 patients in the past 2 years, 20 (3.4%) were referred for MRI testing during their stay in the PCICU. The mean age of the infants was 4.8 ± 3.2 months. Four of the patients were neonates, and eight were postoperative patients. Intracardiac malformations were present in 16 of the infants, vascular rings causing tracheal stenosis in 3 patients, and cardiomyopathy in 1 patient. The mean stay in the PCICU was 28 ± 43 days. Eight of the infants were ventilated, with a mean fraction of inspired oxygen (FiO₂) of 0.30 ± 0.15. Four were receiving inotropic support. All the nonventilated children were intubated for the MRI and extubated in the MRI laboratory. The mean duration of the MRI (door-to-door time) was 110 ± 27 min. All except one patient were hemodynamically stable, and no increase in catecholamine support was necessary during or after the scans. A 10-month-old girl receiving inotropic support needed a single dose of epinephrine due to a short episode of bradycardia after a breathhold for a contrast agent MRI angiography. Mean body core temperature at arrival to the PCICU was 36.8 ± 0.7°C. The mean serum lactate level after the MRI was 1.2 ± 0.4 mmol/l. The mean blood pressure and heart rate before, during, and after MRI were unchanged. The mean diuresis on examination day was insignificantly lower (2.4%) than the day before with unchanged medication (5.09 ± 1.58 vs 5.53 ± 1.77 ml/kg/h). For 14 (70%) of the 20 patients, surgical or catheter interventional procedures were initiated based on novel MRI information. Conclusion Cardiac MRI can be performed safely with low risk and limited hemodynamic changes for infants during their stay in the PCICU. Cardiac MRI provides key information for invasive management decisions in this subset of patients.