Patients with multiple sclerosis and Parkinson's disease may experience pelvic floor dysfunction and constipation which can affect ileoanal pouch emptying. This can lead to complications such as pouchitis, pouch dysfunction, and failure. We hypothesized that patients with neurological diseases have a higher rate of pouch failure and complications than healthy controls. Data were sourced from the institutional ileoanal pouch database. Patients with multiple sclerosis or Parkinson's disease, diagnosed before or after pouch construction, were matched to a control group of patients without neurological disease using propensity score-optimal matching. Demographics, postoperative and functional outcomes, and quality of life were analyzed. Twenty-six patients (38%) with multiple sclerosis and 16 (62%) with Parkinson's disease were matched with 42 healthy controls. The overall median age was 39 years, median BMI was 25.3kg/m2, and most patients were female (61.9%). Preoperative colorectal diagnoses included ulcerative colitis (83.3%), indeterminate colitis (9.5%), and Crohn's disease (7.1%). Patients with neurological diseases had higher ASA scores (class III, 57.1% vs. 21.4%; p < 0.01), fewer nocturnal bowel movements (median 0 vs. 2; p < 0.001), fewer bowel movements over 24h (median 6 vs. 8; p = 0.01), and were less likely to recommend IPAA construction (72.7% vs. 97%; p = 0.01) than the controls. Other surgical, functional, and quality-of-life outcomes were similar. Patients with multiple sclerosis or Parkinson's disease might differ in pouch function compared with healthy controls. These neurological diseases might affect pouch function. The rate of pouch failure was similar, showing its feasibility despite multiple sclerosis and Parkinson's disease.