Purpose Special needs children presenting with dental problems were penalised during the Covid-19 pandemic due to the reduction of clinical activity and the risks of nosocomial infection. The aim of this study is to evaluate the impact of the pandemic on oral healthcare in paediatric special needs patients. Methods We retrospectively assessed and compared the outpatient clinic activity and dental procedures performed under general anaesthesia in children with special needs at Brescia Children’s Hospital (Italy) in 2019, 2020, and 2021. Any delay between expected waiting time based on assigned priority and surgery was recorded. The efficacy of the protocol adopted to reduce the spread of Covid-19 was evaluated by reporting any infections in patients, parents, and health care providers. Results In 2020, 270 outpatient visits were performed, and 40 patients were treated under general anaesthesia, with a 26% and 65% reduction, respectively, compared to 2019. In 2021, 362 visits were performed (similar to 2019) and 48 patients were treated under general anaesthesia (58% compared to 2019). The mean delay in the planned treatment was 1.0 month in 2019 (pre-pandemic period), 2.1 months in 2020, and 1.1 month in 2021. No cases of Covid-19 infection were reported in the cohort of patients and parents or among the operators related to nosocomial infection. Conclusions The Covid-19 pandemic has profoundly reduced the activity of general anaesthesia in paediatric special need patients during 2020, with a gradual return to normal pre-pandemic activity in 2021. The adopted protocol prevented the spread of COVID-19 during hospitalisation.