This commentary describes the transition to remote delivery of cognitive-behavioral therapy (CBT) for anxiety in children with autism spectrum disorder (ASD) who participates in a clinical trial during the COVID-19 pandemic. The effects of COVID-19 on children's anxiety and on the family functioning are discussed. Modifications to CBT necessitated by telehealth delivery were aimed at maximizing engagement of children and their parents while maintaining treatment fidelity and adhering to the research protocol. Treatment targets were updated to address new sources of anxiety and CBT exposure exercises were modified to accommodate the new reality of quarantine restrictions. If the COVID-19 pandemic continues to affect treatment delivery it may require a widespread utilization of telehealth for treating anxiety in children with ASD.