(1) Background: Celiac disease (CD) can cause long-term inflammation and endothelial dysfunction and has been cited as a risk factor for acute ischemic stroke (AIS) in pediatric patients. However, the rate and outcomes of AIS in pediatric patients with CD has not been explored in a large population. Our objective is to explore the rate, severity, and outcomes of CD amongst pediatric AIS patients on a nationwide level. (2) Methods: The National Inpatient Sample (NIS) database was queried from 2016 to 2020 for pediatric patients with a principal diagnosis of AIS. Patients with a concurrent diagnosis of CD (AIS-CD) were compared to those without (AIS). Baseline demographics and comorbidities, clinical variables of severity, hospital complications, and the rates of tissue plasminogen activator (tPA) and mechanical thrombectomy were compared between the two groups. The main outcomes studied were mortality, discharge disposition, length of stay (LOS), and total hospital charges. (3) Results: Of 12,755 pediatric patients with a principal diagnosis of AIS, 75 (0.6%) had concurrent CD. There were no differences in the severity, discharge disposition, or mortality between the AIS-CD and AIS patients. Patients with AIS-CD were more likely to receive tPA at an outside hospital within 24 h of admission (p < 0.01) and more likely to undergo mechanical thrombectomy (p < 0.01) compared to the AIS patients. (4) Conclusions: CD patients made up only 0.6% of all pediatric AIS patients. No differences in the severity, mortality, or discharge disposition suggests a minimal to absent role of CD in the etiology of stroke. The CD-AIS patients were more likely to receive a tPA or undergo a mechanical thrombectomy; studies are needed to confirm the safety and efficacy of these interventions in pediatric patients.