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Background In Korea, the Korean Community-based Noncommunicable Disease Prevention and Control Program (KCNPC) was implemented in 2012 for the management of patients with chronic diseases. Nineteen primary care clinics, public health centers, and education and consulting centers (ECCs) participated in the implementation of this program. This study assessed the effectiveness of this chronic disease control model by comparing mortality rate and the incidence of complications between patients participating in the KCNPC program and a control group. Methods Using data from the National Health Insurance Service and data from hypertension and diabetes patients registered with 19 ECCs between January 1, 2010 and December 31, 2012, hypertension and diabetes patients who had been treated at a clinic were selected. The final analysis included 252,900 patients, with the intervention group and control group having 126,450 patients each. Survival for the two groups was analyzed using the Kaplan-Meier method. Complications were analyzed using the Cox proportional hazards model. Results The 5-year survival rate in the intervention group (0.88) was higher than that in the control group (0.86). Cox proportional hazards analysis showed that the intervention group had lower risk for mortality (0.84; 95% confidence interval [CI], 0.82–0.86) compared to the control group. Hospitalization due to complications and the proportional risk of hospitalization were also lower in the intervention group. Conclusion The KCNPC model for prevention and control of chronic disease in Korea was found to be effective for hypertension and diabetes patients. Therefore, the KCNPC will be necessary to strengthen the capabilities of local communities, primary medical institutions, and individuals for prevention and control of chronic disease. Expanding the efficient prevention and control policies of the KCNPC to a nationwide scale may be effective as has been demonstrated through limited implementation in some regions., Graphical Abstract