Vaccine hesitancy is a major barrier to vaccination, hindering the success of vaccine efforts and thereby increasing public health risk to viral diseases, including COVID-19. Neurodivergent (ND) individuals, including individuals with an intellectual and/or developmental disability, have demonstrated a heightened risk of hospitalization and death due to COVID-19, highlighting the need for further research specifically on ND communities. We conducted a qualitative analysis using in-depth interviews with medical professionals, non-medical health professionals and communicators, and ND individuals or their caregivers. Using a thematic coding analysis methodology, trained coders identified major themes according to 24 distinct codes spanning across the categories of (1) barriers to vaccination; (2) facilitators to vaccination; and (3) suggestions for improving vaccine confidence. Qualitative findings identify misinformation, perception of vaccine risk, sensory sensitivities, and structural hardship as the most significant barriers to COVID-19 vaccination. We highlight the importance of accommodations to vaccination for the ND community alongside coordinated efforts by healthcare leaders to direct their communities to accurate sources of medical information. This work will inform the direction of future research on vaccine hesitancy, and the development of programs specific to the ND community’s access to vaccines.