Magnetic resonance tissue phase mapping (TPM) has been used to encode voxel-wise myocardial motion velocity in various cardiac diseases. This study aimed to quantify alterations in myocardial motion velocity in the functional ventricle of Fontan patients using TPM and to investigate the relationship between myocardial motion and cardiac function. We prospectively enrolled 28 Fontan patients and 42 age- and sex-matched normal controls. Myocardial motion velocities were assessed using TPM in the longitudinal (Vz), radial (Vr), and circumferential (Vphi) directions. We evaluated the peak velocities, time-to-peak (TTPz, TTPr), and dyssynchrony index (DIz, DIr). Circumferential motion abnormalities were assessed using peak-to-peak (PTP) values, Vphi inconsistency, and twist. Compared to controls, Fontan patients demonstrated significantly reduced peak Vz and Vr during both systole and diastole (all p < 0.001), as well as prolonged systolic TTPz (p = 0.002) and TTPr (p < 0.001). Diastolic DIz was increased (p < 0.001), whereas systolic DIr was decreased (p = 0.04). In multivariable regression analysis, ejection fraction of Fontan patients positively correlated with peak systolic Vr and negatively correlated with mid Vphi PTP (R2 = 0.639). The cardiac output was positively associated with peak systolic Vr and diastolic DIz (R2 = 0.578). TPM may provide quantitative MR biomarkers for regional myocardial motion abnormalities, including impaired myocardial motion velocities, delayed contraction timing, and altered motion synchronization, in Fontan patients. These findings suggest global ventricular dysfunction and may provide insight into the mechanisms underlying reduced ejection fraction and cardiac output in the functional ventricle physiology in Fontan patients.