Hypertension and diabetes mellitus, which induce cardiovascular and cerebrovascular diseases, require government intervention. In South Korea, the web-based registration-and-management system for patients with hypertension and diabetes mellitus was operated as a pilot program. This study explored the experiences of the 71 participating medical centers in G city, South Korea, of using the web-based registration-and-management system for preventing and managing hypertension and diabetes mellitus. After the survey, 40 physicians participated in interviews, and the recorded interviews were analyzed and classified into three categories: participation motivation, participation experiences, and suggestions. The study participants participated in a national pilot project with different expectations. Similar to the survey results on participation experiences, the satisfaction from a patient-care perspective was high, but there was an excessive burden of administrative work from the perspective of primary-medical-center operations. In addition, the suggestions included strengthening systematic education, continuous maintenance, broad project application, and improvements to the system. The system needs to be unified and simplified, the project continuity needs to be secured, and the application of the system to other regions and medical centers needs to be considered to induce public–private cooperation to reduce the amount of administrative work, which is currently excessive.