Providing accurate prenatal prognostication for expectant parents is challenging due to limited literature on factors impacting outcomes in children with congenital aqueductal stenosis (CAS). This study stratified CAS patients into isolated or complex categories (presence of additional intra- or extra-cranial anomalies or genetic syndromes) and evaluated both short- and long-term outcomes. Additionally, the role of ventricular rupture was assessed. This was a single center retrospective-cohort study of CAS patients who underwent fetal MRI over a 10-year period. Of 140 patients with CAS, 107 (76%) were complex and 33 (24%) were isolated. There were no differences in the size of ventricular enlargement or incidence of ventricular rupture between the two groups. 14 pregnancies were terminated, 9 experienced fetal demise/stillbirth, and there were 21 post-natal deaths. Outcomes at the time of hospital discharge were available for 86 patients and long-term follow-up data for 64. CSF diversion (via ventriculoperitoneal shunt) was performed in 95% of complex and 71% of isolated CAS patients. Acutely, no differences were noted in seizures (complex: 10%; isolated: 18%) or respiratory support but there was an increased risk for feeding support. Risks for non-ambulatory status (complex: 32% vs. isolated: 0%), epilepsy (complex: 56% vs. isolated: 19%) and long-term gastrostomy tube assisted feeding (complex: 25.5% vs. isolated: 0%) were significantly greater with complex CAS. The presence of rupture did not impact clinical outcome. Poor clinical outcome was associated with complex CAS. Ventricular rupture alone did not portend a poor outcome. Prenatal counseling can tailor prognostication by CAS type.