Background: Adhering to Clinical Practice Guidelines (CPGs) serves as the driving force behind making decisions based on the best evidence and making efforts for improving the quality of patient care and outcomes. In 2010, promoting the quality of clinical care through implementing CPGs was turned into a priority health policy in Iran as in many other countries. Despite requiring Iranian hospitals to implement CPGs in January 2017, the concept and implementation method of CPGs remained to be clarified. This action research focuses on acquiring an in-depth understanding of how to define and implement CPGs in a selected general hospital in Iran.Methods: This study employs Soft Systems Methodology (SSM) as a commonly-used approach for tackling complex problems with social, political and human dimensions. Given the inherent roles of technical processes, organizational culture, and personnel’ perspectives in providing clinical care, implementing CPGs was considered a complex problem situation, and conceptualized by use of a purposeful activity model. We will conduct semi-structured in-depth interviews and hold group discussions with different stakeholders to enquire into the situation. Moreover, we will use SSM tools and techniques to identify the main areas of changes, and select necessary measures to facilitate the implementation of CPGs. Flexible qualitative methods of data collection and analysis are utilized throughout the study.Discussion: Applying SSM in implementing CPGs can generate knowledge by recognizing hyper-complexity in healthcare setting, adopting an attitude of inquiry, and fostering dynamic changes in diverse and numerous worldviews of professionals in the accommodation process. This knowledge can provide a model for the successful implementation of CPGs at a macro-system level and facilitate the persuasion process at the hospital mesosystem level. More importantly, adopting SSM can create iterative learning loops over time and thus help the actors of clinical microsystems face future healthcare complexities.