Engaging patients in the self-management decision-making provides opportunities for positive health outcomes. The process of shared decision making (SDM) is touted as the pinnacle of patient-centred care, yet it has been difficult to implement in practice. Access to tools resulting from the integration of all health data and clinical evidence, and an ease of communications with care providers are needed to engage patients in decision making. Personal health record (PHR) technology is a promising approach for overcoming such barriers. Yet there is a scarcity of studies on system design for SDM via PHR. This paper describes a study protocol to identify functional requirements of PHR for facilitating SDM and factors that would influence the embedding of the proposed system in clinical practice.