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The right to the highest attainable standard of health is a fundamental human right and, central to this right within a hierarchical health system, is the existence of a well-functioning referral system that allows for continuity of care across the different tiers of care. A referral system enables management of client health needs comprehensively with resources locally unavailable. This study sought to establish challenges facing implementation of the referral system for quality health care services in Kiambu County, Kenya. Specifically, investigated the influence of infrastructure, capacity of health care workers, health information systems and financial resources on implementation of health care referral system. A crosssectional research design was done targeting health care workers in public health care facilities Tier 2 and Tier 3 in Kiambu County and two hundred and seventy one respondents took part in the study. A statistical analysis was done using SPSS 20 and Excel 2013. Both questionnaires and interview guide were employed as data collection tools which attained quantitative and qualitative data. Inferential statistics was used to conduct regression analysis. From the findings of the study it was established there existed a relationship between independent and dependent variables as revealed by infrastructure with coefficient 4.457; capacity of health care workers with coefficient 4.105; health information systems with coefficient 4.405; and financial resources with coefficient.4.013. The p value was <0.001. The study concluded that infrastructure, health information systems, capacity of health care workers, and financial resources are challenges in implementation of health care referral system in Kiambu County and should be strengthened. The study recommended that Kiambu County Health care facilities should improve infrastructure; implement a standard referral system monitoring toolkit and curriculum to train health workers on the referral policies and guidelines; develop standard referral forms/registers and provide adequate funds for implementation monitoring and evaluation.