We aimed to investigate Fontan associated liver disease in children by shear wave elastography (SWE). This is a single-center, prospective case-control study included 41 patients with Fontan physiology and 30 healthy controls. Hepatic and splenic shear wave elasticity values were exhibited both as kPa and m/s. The mean hepatic SWE values of Fontan patients (n = 41; 15.8 +/- 3.2 kPa or 2.5 +/- 1.8 m/s) were significantly higher than the control group (n = 30; 5.59 +/- 0.6 kPa or 1.37 +/- 0.07 m/s) (P < 0.001). The mean splenic SWE values of Fontan patients were (25.6 +/- 4.61 kPa or 2.85 +/- 0.22 m/s) significantly higher than the control group (15.9 +/- 1.44 kPa or 2.29 +/- 0.1 m/s) (P < 0.001). There were statistically significant positive correlations among the follow-up duration after the Fontan procedure with NT-proBNP (P = 0.008, r = 1) and prothrombin time (P = 0.009, r = 0.4) as well as the hepatic SWE values with alanine aminotransferase (P = 0.039, r = 0.32), gamma-glutamyl transferase (P = 0.045, r = 0.31), and PT (P = 0.011, r = 0.39). There has been statistically significant moderate positive correlations of splenic stiffness values with PT (P = 0.047, r = 0.34), and INR (P = 0.038, r = 0.35). The sensitivity and specificity of liver stiffness cutoff value as 11.1 kPa for detection of Fontan associated liver disease were 95% and 100%, respectively. The hepatic and splenic stiffness increase independently in Fontan patients due to parenchymal disease. Hepatic SWE is a reliable and noninvasive predictor of early hepatic alterations that could not be detected only by biochemical results or routine ultrasound examinations.