We conducted a study to determine whether patients born with Trisomy 21 and left-to-right shunts who develop pulmonary vein stenosis (PVS) have a longer exposure to shunt physiology compared to those who do not develop PVS. We included patients seen at Boston Children’s Hospital between 15 August 2006 and 31 August 2017 born with Trisomy 21 and left-to-right shunts who developed PVS within 24 months of age. We conducted a retrospective 3:1 matched case–control study. The primary predictor was length of exposure to shunt as defined as date of birth to the first echocardiogram showing mild or no shunt. Case patients with PVS were more likely to have a longer exposure to shunt than patients in the control group (6 vs. 3 months, p-value 0.002). Additionally, PVS patients were also more likely to have their initial repair ≥ 4 months of age (81% vs. 42%, p-value 0.003) and have a gestational age ≤ 35 weeks (48% vs. 13%, p-value 0.003). Time exposed to shunts may be an important modifiable risk factor for PVS in patients with Trisomy 21.