Primary care is not well established in Korea despite its importance in population health. To reinforce the primary care system, understanding the public view of primary care will be essential. We aimed to compare the public perception of primary care qualities across types of healthcare facilities. We conducted a cross-sectional, web-based survey at a university in Seoul, South Korea, from October 2018 to February 2019. Using the Korean Primary Care Assessment Tool (K-PCAT), participants assessed the qualities of primary care services provided by the university health service (a university-based, patient-centered primary care model), community clinics, and hospitals. We compared K-PCAT scores across facilities and evaluated the factors associated with the differences using general linear models. A total of 5,748 responses were analyzed. K-PCAT total scores were highest for the university health service (61.0 ± 15.9) and lowest for hospitals (48.1 ± 14.5), with significant differences between facilities (P < .001). The university health service received the highest scores for first contact, comprehensiveness, personalized care, and family/community orientation; community clinics for continuity of care; and hospitals for care coordination and trust/satisfaction. Primary care facilities were rated higher than hospitals by individuals in good health, with low income levels, using ambulatory care more frequently, and spending less on medical expenses. In conclusion, the user-perceived primary care quality was higher for community-based primary care facilities than hospitals. The highest score was for the university health service, suggesting that setting-based, patient-centered primary care would be an effective model for restructuring the primary care system in Korea.