Objectives: Children and young people (CYP) with special educational needs (SEN) are more likely to experience disturbed sleep and poor mental wellbeing. This study explored the differential impact of the coronavirus disease 2019 (COVID-19) pandemic on the sleep and mental wellbeing of CYP with and without SEN. Methods: The National Institute of Health Research Children and Young People MedTech Cooperative, Sheffield Children’s National Health Service (NHS) Foundation Trust, and The Sleep Charity carried out an online survey between June 23, 2020, and August 17, 2020. The 77-item survey was shared on social media platforms. Results: A total of 559 participants were included in the analyses, and 15.74% of them reported having CYP with SEN. While sleep changes due to the pandemic were largely similar for both groups, CYP with SEN were more likely to get up or wake up during the night than those without SEN (40.91% vs. 27.18%). CYP with SEN were significantly more likely than those without SEN to be demotivated (61.44% vs. 31.57%), sad and tearful (36.15% vs. 19.35%), or anxious and stressed (41.67% vs. 18.54%) during the pandemic, and the increased anxiety was more likely to contribute to poorer sleep (43.48% vs. 14.82%). Conclusions While the majority of CYP in both groups reported sleep changes due to the pandemic, CYP with SEN experienced more sleep disturbance. The findings provide initial evidence to suggest that the pandemic may have had a greater impact on the sleep and mental wellbeing of CYP with SEN than those without SEN.