Background Biliary atresia (BA) is a rare obliterative cholangiopathy and Kasai portoenterostomy (KP) represents its first-line treatment; clinical and laboratory parameters together with abdominal ultrasound (US) are usually performed during the follow-up. Shear-wave elastography (SWE) is able to evaluate liver parenchyma stiffness; magnetic resonance imaging (MRI) has also been proposed to study these patients. Purpose To correlate US, SWE, and MRI imaging findings with medical outcome in patients with BA who are native liver survivors after KP. Material and Methods We retrospectively enrolled 24 patients. They were divided in two groups based on “ideal” (n = 15) or “non-ideal” (n = 9) medical outcome. US, SWE, and MRI exams were analyzed qualitatively and quantitatively for imaging signs suggestive of chronic liver disease (CLD). Results Significant differences were found in terms of liver surface ( P = 0.007) and morphology ( P = 0.013), portal vein diameter ( P = 0.012) and spleen size ( P = 0.002) by US, liver signal intensity ( P = 0.013), portal vein diameter ( P = 0.010), presence of portosystemic collaterals ( P = 0.042), and spleen size ( P = 0.001) by MRI. The evaluation of portal vein diameter (moderate, κ = 0.44), of portosystemic collaterals (good, κ = 0.78), and spleen size (very good, κ = 0.92) showed the best agreement between US and MRI. A significant ( P = 0.01) difference in liver parenchyma stiffness by SWE was also found between the two groups (cut-off = 9.6 kPa, sensitivity = 55.6%, specificity = 100%, area under the ROC curve = 0.82). Conclusion US, SWE, and MRI findings correlate with the medical outcome in native liver survivor patients with BA treated with KP.