Background: Congenital heart disease (CHD) is one of the most important and common group of congenital malformations in humans. Concurrent development and close functional links between the fetal heart and placenta emphasise the importance of understanding placental function and its influence in pregnancy outcomes. The aim of this study was to evaluate placental oxygenation by relaxometry (T2*) to assess differences in placental phenotype and function in CHD. Methods: In this prospective cross-sectional observational study, 69 women with a fetus affected with CHD and 37 controls, whole placental T2* was acquired using a 1.5-Tesla MRI scanner. Gaussian Process Regression was used to assess differences in placental phenotype in CHD cohorts compared to our controls. Results: Placental T2* maps demonstrated significant differences in CHD compared to controls at equivalent gestational age. Mean T2* values over the entire placental volume were lowest compared to predicted normal in right sided obstructive lesions (RSOL) (Z-Score 2.30). This cohort also showed highest lacunarity indices (Z-score −1.7), as a marker of lobule size. Distribution patterns of T2* values over the entire placental volume were positively skewed in RSOL (Z-score −4.69) and suspected, not confirmed coarctation of the aorta (CoA-) (Z-score −3.83). Deviations were also reflected in positive kurtosis in RSOL (Z-score −3.47) and CoA- (Z-score −2.86). Conclusion: Placental structure and function appear to deviate from normal development in pregnancies with fetal CHD. Specific patterns of altered placental function assessed by T2* deliver crucial complementary information to antenatal assessments in the presence of fetal CHD.