Background: Flares of autoimmune conditions can happen after coronavirus disease 2019 (COVID-19) infection and after COVID-19 vaccines. Patients and clinicians confront difficult decisions about vaccine safety when considering efforts to balance the risks of disease exacerbation after vaccines versus the protection that vaccines offer to potential serious life-threatening complications of COVID-19 infection. Objective: To examine symptom flares after COVID-19 infection and vaccines in the case of a form of autoimmune encephalitis that primarily affects children and young adults (pediatric acute-onset neuropsychiatric syndrome [PANS] / pediatric autoimmune neuropsychiatric disorders associated with streptococcal infections [PANDAS]). Method: A cross-sectional study that used a survey distributed through PANS/PANDAS groups, organizations, and clinics. Results: Surveys were completed by 496 parents and/or caregivers of children with PANS/PANDAS. Among the children reported to have had a COVID-19 infection (n = 178), 43% reported severe flares of PANS/PANDAS symptoms, 23% reported mild flares, and 30% reported no symptom flares. Among those who had received COVID-19 vaccines (n = 181), 65% observed no changes in PANS/PANDAS symptoms after the vaccine, 19% reported mild flares, and 15% reported severe flares. Paired sample t-tests showed that, after COVID-19 infections, children with PANS/PANDAS were significantly more likely to experience a severe symptom flare than a mild flare or no change in symptoms. In contrast, after receiving COVID-19 vaccines, children were significantly more likely to experience no change in PANS/PANDAS symptoms than to endure a mild or severe symptom flare. In addition, children who recovered from PANS/PANDAS were significantly more likely to have no symptom change versus children who were managing the condition, both after COVID-19 infection (92% versus 25%) and vaccine receipt (100% versus 66%). Conclusion: These results support COVID-19 vaccination for most individuals with PANS/PANDAS given that the frequencies of symptom flares and setbacks after COVID-19 infection were significantly higher than after the COVID-19 vaccine. Nonetheless, further studies are needed to fully assess the risk-benefit balance and to provide a more individualized approach to disease prevention in people with immune vulnerabilities.