Both cardiac magnetic resonance (CMR) and cardiac catheterization (cath) may assess patients with single ventricle physiology prior to stage II or Fontan palliation. However, development of significant aortopulmonary collaterals may invalidate assumptions of the Fick method. We compared CMR and cath flow measurements and evaluated the relation to collateral flow. This single-center study included all pre-stage II and pre-Fontan patients between 2010 and 2017 with CMR and cath within 1month. Pulmonary (Qp) and systemic flow (Qs) by cath were calculated by Fick method. CMR Qp was calculated by total pulmonary venous flow, and Qs by total vena caval flow. Collateral flow by CMR was the difference of pulmonary vein and pulmonary artery flow. In 26 studies (16 pre-stage II and 10 pre-Fontan) in 21 patients, collateral flow was higher in pre-Fontan patients (1.8 ± 0.6 vs 0.9 ± 0.8L/min/m2, p = 0.01). Overall, CMR and cath had good agreement for Qs and Qp:Qs, with moderate correlation (r = 0.44, p = 0.02 for Qs, r = 0.48, p = 0.02 for Qp:Qs). In pre-Fontan but not in pre-stage II patients, CMR had higher Qp (mean difference - 1.71L/min/m2) and Qp:Qs (mean difference - 0.36). The underestimation of cath Qp correlated with amount of collateral flow (r = - 0.47, p = 0.02). Neither cath nor CMR flow measurements correlated with outcomes in this small cohort. In conclusion, collaterals lead to systematically higher Qp and Qp:Qs measurements by CMR vs cath in single ventricle patients. Measurements may not be used interchangeably, with potential clinical significance in estimating pulmonary vascular resistance. Further study is necessary to evaluate possible relation to clinical outcomes.