Congenital heart disease (CHD) is a term which includes a range of developmental cardiac diseases with severe health impacts. In the past, research has solely focused on improving medical outcomes for individuals with CHD and has successfully increased the chance of survival. To date, there has been little research on the mental health of this population. Existing research has examined cardiac physiology in adults with anxiety disorders. However, limited to no research has explored cardiac physiology in individuals with CHD, more specifically in children with CHD. The present study examined the connection between measures of heart rate variability (HRV) and anxiety-related constructs in children with CHD and typically developing children. Eighty-one children (40 diagnosed with CHD; 41 typically developing) ages 7 to 16 years (mean age = 11.7, SD = 2.38) completed a battery of cardiac and anxiety measures. We hypothesized that children with CHD would demonstrate significantly lower HRV and significantly higher levels of anxiety than typically developing children. Results demonstrated significantly lower primary time domain HRV measures and primary frequency domain HRV measures as well as higher LF/HF ratio than typically developing children. The current study was the first of its kind to explore time and frequency domain measures of HRV with anxiety, anxiety sensitivity, intolerance of uncertainty, and health anxiety in this population of Canadian children with CHD. Information gleaned from the current study will contribute to the understanding of psychopathology in this specialized medical population.