Background: To discriminatively evaluate the cost-saving effects of a disease management program for diabetic nephropathy patients through care process rectification and, subsequently, improved health outcomes. Methods: This study links public medical insurance claims data to the health records of a disease management program for diabetic nephropathy patients. To account for selection bias caused by the non-randomized allocation of the disease management program for diabetes patients, we adopted a fixed-effect model of panel data analysis. To discriminatively evaluate the cost-saving effects of the disease management program for diabetic nephropathy patients through care process rectification and, subsequently, improved health outcomes, we expanded the difference-indifferences analysis from the traditional two-period model to a three-period model, comprising the before-intervention, during-intervention, and after-intervention periods. Data were extracted from municipal public insurers in Kure, Japan. Results: The cost-reduction effect in terms of treatment costs from the before-intervention period to the duringintervention period (the rectification effect) was 4.02%, and the cost-saving effect from the during-intervention period to the after-intervention period (the health improvement effect) was 2.95%. Conclusions: A disease management program for diabetes patients organized by local public insurers in Japan reduced costs both by amending treatment processes and by subsequently improving the prognosis of the disease.