The COVID-19 pandemic has strained the resources of the world's healthcare systems. Most individuals with neurodevelopmental disabilities (NDDs) experience significant mental health issues and face substantial barriers in accessing appropriate supports which have been exacerbated during the pandemic. It is unknown the extent to which COVID-19 impacted the demand for and effectiveness of inpatient care for those with NDDs. The impact of COVID-19 on the number of admissions of youth with NDDs to pediatric inpatient psychiatry units, as well as their functioning and length of stay during the first two years of the pandemic was analyzed using Bayesian structural time series models. Admission data of youth with NDDs from four pediatric inpatient units in Alberta, Canada (n = 2144) was examined. Inpatient admissions of youth with NDDs significantly increased following the onset of the pandemic. Compared to the period prior to the pandemic, patients with NDDs had significantly worse overall functioning and received fewer days of treatment. These findings highlight the need for increased resources to support the mental health needs of this vulnerable population and are consistent with other studies in the general population examining the utilization of inpatient psychiatric units during the pandemic.