The reprocessing of gastrointestinal endoscopes and accessories, including pre-cleaning, cleaning, high-level disinfection, rinsing, drying, and storage, is essential for preventing infections during endoscopic procedures. The risk of infection is significantly minimized when these processes are performed properly. However, the reprocessing environment in primary care settings differs from that in endoscopy centers, and ongoing advancements in medical practices and reprocessing technologies highlight the need for updated, context-specific guidelines. The Korean Academy of Family Medicine has developed these guidelines, tailored to the unique conditions of primary care settings, through a comprehensive review of both international and local standards, as well as systematic reviews of relevant literature. This guideline presents step-by-step procedures and key principles for effective endoscope reprocessing, with a focus on the needs of primary care institutions. By adhering to these guidelines, primary care physicians can maintain the highest standards of safety and effectiveness, minimize infection risks, and promote optimal clinical outcomes.