Background: Infections are hypothesized to trigger certain autoimmune diseases; however, data surrounding incidence trends of pediatric neuro-autoimmune disorders during the COVID-19 pandemic are lacking. Our retrospective study thus assessed the incidence of pre-defined autoimmune disorders diagnosed at the Children’s Hospital of Eastern Ontario in Ottawa, Canada between October 2017 and June 2023. Methods: Inpatient and outpatient charts were queried to identify subjects with neuro-autoimmune disorders or type 1 diabetes (T1D) as a non-neurological autoimmune comparison group. Monthly incidences were calculated and grouped based on three COVID-19 pandemic restriction periods: the pre-restrictions period (October 2017-March 2020), intra-restrictions period (April 2020-June 2022), and post-restrictions period (July 2022-June 2023). Poisson regression models were fit to the incidence data. Results: New diagnoses of neuro-autoimmune disorders and T1D were identified in 86 and 591 subjects, respectively. Incidence of neuro-autoimmune disorders decreased significantly during the intra-pandemic restrictions period when compared to the pre-pandemic period (IRR=0.56, 95% CI: 0.32-0.93, P<0.05). Albeit not statistically significant, the incidence then increased to higher than pre-pandemic levels during the post-restrictions period. T1D showed no significant changes in incidence. Conclusions: Incidence of neuro-autoimmune disorders, but not T1D, decreased during COVID-19 pandemic restrictions, which may be due to reduced transmission of key infectious triggers.