Little research attention has been paid to the occurrence of heart failure (HF) in children with complex congenital heart diseases (CHDs). Herein, we describe the prevalence, risk factors, and costs associated with HF in complex CHD. Patients aged ≤17 years and diagnosed with a complex CHD on multiple service visits over a 15-year period in the SC Medicaid dataset (1996–2010) were tracked and analyzed. The cohort included 2999 unduplicated patients; 51.0% were male; 34.4% were African American. HF was diagnosed in 7.6%. Single ventricle lesions, genetic syndromes, and ventricular arrhythmia were significantly associated with an increased likelihood of being diagnosed with HF, controlling for development of comorbid pulmonary hypertension. Patients with HF received significantly more subspecialty care, more surgeries, more hospitalizations, more total days of inpatient care, and more emergency department care than those without HF. Patients with significantly higher total care costs paid by Medicaid had HF, more cardiac surgeries, and more specialized mechanical or other support procedures, controlling for diagnosed single ventricle CHD, a genetic syndrome, and number of non-cardiac surgeries. Complex CHD patients with HF incur significantly higher care costs but require multifaceted, intensive supports for management of incident complications and comorbid conditions.