Background Integrated care has important implications for children with medical complexity (CMC) who rely on care and service delivery involving multiple providers in different places over time. Most studies describing complex care programmes focus on the effectiveness of care co‐ordination rather than the process of system integration. This pilot study explores the implementation process of the Integrated Complex Care Model: a voluntary partnership between acute, rehabilitative and community care aimed at system integration through a key worker model to improve care co‐ordination for CMC. Methods This descriptive study used qualitative analyses and syntheses to explore the process of inter‐organizational collaboration under ‘real‐life’ circumstances. Multiple methods and sources of data were gathered to support triangulation in understanding of enablers and barriers to model implementation. Forty hours of meeting minutes and administrative databases housing patient records were reviewed. Baseline demographic information was available for 23 families, including child health‐related quality of life and healthcare utilization. A subset of 12 parental caregivers and 21 additional key informants participated in individual interviews or focus groups. Findings are presented using King and Meyer's description of system integration and care co‐ordination. Results Model enablers included dedication, timing, leadership and electronic care plan use/communication among key workers, families and health providers. Barriers included assumptions about partner organizations, differing organizational structures and client information systems, constrained project resources and limited engagement of primary care. Parents perceived an electronic care plan as a facilitator of timely and effective care for CMC across multiple settings. Conclusions At a systems level, the integrated model fostered collaboration between partner organizations. At a family level, development of inter‐organizational management structures and communication platforms; provision of adequate resourcing; and increased engagement of primary care may enable high level organizational integration aimed at improved care co‐ordination for CMC.