Purpose Children with Special Health Care Needs (CSHCN) may experience disruptions in education due to extended hospitalizations. The purpose of this study was to describe how CSHCN experience educational supports during inpatient rehabilitation and identify the ongoing challenges when planning to return to school. Materials and methods Semi-structured focus groups were conducted with parents (n = 12), former patients (n = 20), and rehabilitation professionals (n = 8). Results Through qualitative thematic analysis based on descriptive phenomenology, we developed three themes: 1) Inpatient educational support such as instruction and schoolwork helped reduce the learning loss during hospitalization. However, these supports were sometimes complicated by lags in school approvals and challenges in coordination between systems. 2) Transition planning involved establishing necessary services to support CSHCN’s educational and healthcare needs at school re-entry. However, families reported limited information and guidance as key barriers. 3) Dynamic courses of school re-entry required continued support after discharge. The participants recommended that reassessment and adjustment of transition plans were often necessary to account for evolving developmental and educational needs but were not always received. Conclusions There is an ongoing need to improve communication between clinicians and educators, information for families, and long-term follow-up on the changing educational needs for CSHCN after rehabilitation.