Hypoplastic Left Heart Syndrome is a congenital heart disease that leads to a single ventricle (SV) circulation. A multitude of complications can occur with the existing three-stage palliative operation leading to 50% survival rates. The hybrid comprehensive stage II operation (HCSII) was designed for a subset of SV patients [1]. The operation results in a stent under systemic pressure on its outer surface and “Glenn” pressure on its inner surface. The study objective is to determine if these unusual stresses result in excessive deformation and limited lifetime. A benchtop mock flow loop (MFL) was designed to mimic the circulatory system of patients with a BSA ~0.34m2. The model includes a patient-derived 3D print of the relevant HCSII anatomy, incorporating an intra-pulmonary homograft baffle between the left and right pulmonary ostia supported by a Palmaz Genesis 2510B stent. The four-compartment MFL is based on a reduced lumped-parameter model of the HCSII circulation and is tuned to match post-operative cardiac catheter reports of two patients. A digital otoscope is used to perform in-situ tracking of stented baffle motion under pulsatile loading condition from the main pulmonary artery (MPA). A scanning electron microscope and a multi-featured tracker algorithm with principal component analysis are utilized to characterize and quantify coupled stent-baffle cyclic deformation in pulmonary artery locations. In-silico modeling was carried out by means of finite element analysis in Abaqus to cross-validate the experimental deformation results. The displacement of the stent is tracked in all locations throughout the cycles. Throughout the cardiac cycle, mean displacement, deformation, and strain ranges from 0.05–0.4 mm, 0.01–0.1 mm, and 0–0.25, respectively. In-silico findings cross-validate in-vitro results, showing minimal stent deformations, ensuring pulmonary flow remains unaffected. Fatigue analysis indicates stent integrity endures a minimum of ~2.81e15 cardiac cycles at the critical sections of the stent.