BACKGROUND: Little is known about the provision of care coordination to children with medical complexity (CMC) and their families in Japan. The aim of this study was to describe provision of care coordination and explore the factors associated with quality of care coordination for Japanese CMC and their families. METHODS: We used an exploratory cross-sectional study design. Participants were recruited at a children's hospital located in one prefecture, Japan. Primary caregivers raising children aged between <1 and 20 years and receiving reimbursements for their home-based medical care at a children's hospital were eligible to participants in this study. The study examined the relationship between parents' ratings of care coordination as 'adequate,' 'inadequate' or 'not received' and characteristics of children, parents, and families. RESULTS: Ninety-nine parents caring for CMC were included in the analysis. Of those, 22.2% reported their child had a care coordinator. Caregivers were divided into three groups depending on the quality of care coordination: Group 1 reported adequate care coordination; Group 2 reported inadequate care coordination; and Group 3 had no need for care coordination. We compared the socio-demographics of children, parents and families, their service use and the health-related quality of life (HR-QOL) and caregiver burden scores of parents across the three groups. The parents' free time, access to timely care for children and service satisfaction were positively associated with adequate care coordination for CMC and their families. CONCLUSIONS: Providing adequate care coordination for CMC and their families is essential for access to timely services and more positive psychological health of parents. High quality care coordination for CMC and their families is urgently needed in Japan.