We sought to evaluate contractile function in single-ventricle patients before and after imposition of Fontan physiology. Single right ventricle (SRV; n = 38) and single left ventricle (SLV; n = 11) patients underwent cardiac magnetic resonance imaging pre and post Fontan operation. Global radial strain (GRS), global circumferential strain (GCS), and global longitudinal strain were measured along with ejection fraction (EF) and atrioventricular valve regurgitation (AVVR). Age at cardiac magnetic resonance imaging before the Fontan operation was 3.1 ± 1.3 years and after the Fontan procedure was 5.8 ± 2.7 years. There were no significant EF differences between SRV and SLV patients before and after the Fontan procedure, and EF did not deteriorate significantly after the Fontan operation. GRS was significantly lower for SRV patients than for SLV patients before (24.3% vs 32.1%; P = .048) and after (21.8% vs 29.7%; P = .045) the Fontan procedure. GRS and GCS of the SRV patients deteriorated significantly after the Fontan operation (GRS, P = .01; GCS, P = .009). Strains showed positive correlations before and after the Fontan operation with positive correlations among each strain. Within all patients, strains correlated positively with EF. Strains and EF negatively correlated with AVVR (GRS P = .03, r = −0.22; GCS P = .03, r = −0.23; EF P < .001, r = −0.37). Strains were lower for SRV than for SLV patients before and after the Fontan operation and deteriorated after the Fontan operation. Our study suggests that strain measures might detect ventricular deterioration earlier than EF. Because strains before and after the Fontan operation were positively correlated, and negatively correlated with AVVR, the early institution of myocardial protective therapy including AVVR management, especially for SRV patients, might have benefit.