Background: Children with cerebral palsy (CP) place a considerable burden on medical costs and add to an increased number of inpatient days in Taiwan. Continuity of care (COC) has not been investigated in this population thus far. Materials and Methods: We designed a retrospective population-based cohort study using Taiwan's National Health Insurance Research Database. Patients aged 0 to 18 years with CP catastrophic illness certificates were enrolled. We investigated the association of COC index (COCI) with medical costs and inpatient days. We also investigated the possible clinical characteristics affecting the outcome. Results: Over five years, children with CP with low COCI levels had higher medical costs and more inpatient days than did those with high COCI levels. Younger age at CP diagnosis, more inpatient visits one year before obtaining a catastrophic illness certificate, pneumonia, and nasogastric tube use increased medical expenses and length of hospital stay. Conclusions: Improving COC reduces medical costs and the number of inpatient days in children with CP. Certain characteristics also influence these outcomes.