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Objectives To identify barriers and facilitators that influenced the implementation of paediatric clinical pharmacy service (CPS) in Hong Kong’s public hospitals from clinical pharmacists’ perspective. Methods A qualitative study based on semi-structured interviews of clinical pharmacists who practiced in paediatrics in public hospitals in Hong Kong. Interview schedule was designed based on determined themes identified in previous research and pilot testing was performed. The coding process was performed by two researchers with the resulting topics organised by thematic analysis. Consensus was reached amongst the researchers for the identification of themes that emerged during the interviews. The Consolidated Criteria for Reporting Qualitative Research guideline was followed to ensure the complete and transparent reporting of this research. Ethical approval for this study was obtained from the research ethics committee of the relevant institutions. Key findings Of the 32 clinical pharmacists from across the study sites, 12 were interviewed. Five barriers and three facilitators were identified as main themes. The barriers that were identified which hindered service implementation include the service penetration into the healthcare system, practice environment constraints, lack of affirmation from the administrative stakeholders, governance of the profession and partnership with universities. The facilitators that were identified which enabled service implementation include other healthcare professionals’ trust and confidence in the service, the support from the pharmacy management team and clinical pharmacists’ self-efficacy. Conclusions Clinical pharmacists interviewed reported that the successful implementation of CPS in paediatrics in public hospitals in Hong Kong is an area of continued development with several key barriers identified.