Background: Infections are hypothesized to trigger certain autoimmune diseases; however, there is a lack of epidemiologic data surrounding pediatric neuro-autoimmune disorders during the COVID-19 pandemic. Our retrospective study assessed the incidence of pre-defined autoimmune disorders at the Children’s Hospital of Eastern Ontario from October 2017-June 2024. Methods: Inpatient/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 compared between three COVID-19 pandemic restriction periods: the pre-restrictions (October 2017-March 2020), intra-restrictions (April 2020-June 2022), and post-restrictions periods (July 2022-June 2024). Poisson regression models were fit to the incidence data. To evaluate incidence of specific neuro-autoimmune disorders, crude monthly incidences of six diagnosis categories were compared: ‘Guillain-Barré syndrome’, ‘anti-NMDAR encephalitis’, ‘juvenile dermatomyositis’, ‘multiple sclerosis (MS)’, ‘acute demyelinating disorders’, and ‘other’. Results: Incidence of neuro-autoimmune disorders, but not T1D, decreased during the intra-restrictions period compared to the pre-restrictions period (IRR=0.57, 95% CI: 0.33-0.95, P<0.05). Grouping neuro-autoimmune subjects by diagnosis category showed a trend towards decreased incidence during the intra-restrictions versus pre-restrictions periods for all groups except MS. Conclusions: Incidence of certain neuro-autoimmune disorders, but not MS and T1D, decreased during pandemic restrictions, which may be due to reduced transmission of key infectious triggers.