OBJECTIVE The objective was to quantify risks of hydrocephalus, cerebrospinal fluid (CSF) shunt placement, and shunt malfunction in children < 3 years of age with congenital heart defect (CHD) versus matched controls. METHODS This was a multicenter retrospective cohort study conducted using TriNetX. Children < 3 years with CHD were propensity score matched 1:1 to controls on the basis of demographic characteristics and comorbidities. Outcomes were hydrocephalus (ICD-10 code G91), CSF shunt placement, and shunt malfunction (ICD-10 T85.0). Associations were reported as risk ratios (RRs) with 95% confidence intervals (CIs). RESULTS Of 83,258 children with CHD and 418,476 controls, matching yielded 64,413 per group with excellent balance (all standardized mean differences < 0.02). Compared to matched controls, CHD patients were associated with higher rates of hydrocephalus (1.1% vs 0.2%, RR 4.98, 95% CI 4.15–5.97), shunt placement (0.4% vs 0.04%, RR 9.11, 95% CI 6.12–13.55), and shunt malfunction (2.5% vs 0.4%, RR 5.75, 95% CI 5.07–6.53) (all p < 0.001). Across physiology, elevations were consistent; within CHD, the rate of shunt malfunction was higher in patients with cyanotic defects than those with acyanotic defects (4.6% vs 2.5%, RR 1.86, 95% CI 1.61–2.14, p < 0.001). The strongest associations were observed in defect types most frequently encountered during the first 3 years of life. Hydrocephalus risk was increased in patients with patent ductus arteriosus (PDA) (2.2% vs 0.4%, RR 5.12, 95% CI 3.93–6.68), atrial septal defect (ASD) (1.1% vs 0.3%, RR 4.47, 95% CI 3.65–5.47), atrioventricular septal defect (AVSD) (1.0% vs 0.2%, RR 4.32, 95% CI 3.57–5.23), ventricular septal defect (VSD) (0.9% vs 0.3%, RR 2.79, 95% CI 2.01–3.88), and coarctation (2.1% vs 0.6%, RR 3.50, 95% CI 1.74–7.05). Shunt placement was likewise more common in patients with PDA (0.8% vs 0.1%, RR 9.14, 95% CI 5.27–15.87), ASD (0.4% vs 0.1%, RR 7.84, 95% CI 5.17–11.89), AVSD (0.4% vs 0.05%, RR 7.85, 95% CI 5.22–11.80), and VSD (0.3% vs 0.1%, RR 4.33, 95% CI 2.31–8.11) (all p < 0.001). Shunt malfunction was most pronounced in patients with tetralogy of Fallot (7.4% vs 0.7%, RR 11.30, 95% CI 5.94–21.49) and coarctation (6.8% vs 0.6%, RR 11.60, 95% CI 6.10–22.05) and remained elevated across septal lesions (AVSD 2.5%, ASD 2.4%, and VSD 3.1%) and PDA (3.8%) (all p < 0.001). CONCLUSIONS CHD is associated with increased risk of hydrocephalus, shunting, and shunt malfunction in early childhood. Risks increase with septal lesions, PDA, and coarctation, with a higher rate of shunt malfunction in patients with cyanotic physiology. These findings support early cardiology-neurosurgery surveillance and care.