Background: The Renal Health Program (RHP) was implemented in 2013 as a secondary prevention strategy to reduce the incidence of patients initiating dialysis and overall mortality. A previous study found that adherent patients have 58% protection against progression to dialysis compared to non-adherent. The main objective of the study was to estimate the lifetime economic and health consequences of the RHP intervention to determine its cost-effectiveness in comparison with usual care. Methods: We use a Markov model of three health stages to simulate disease progression among chronic kidney disease patients in Lima, Peru. The simulation time-horizon was 30 years to capture the lifetime cost and health consequences comparing the RHP to usual care. Costs were estimated from the payer perspective using institutional data. Health outcomes included years lived free of dialysis (YL) and quality adjusted life years (QALY). We conducted a probabilistic sensitivity analysis (PSA) to assess the robustness of our estimates against parameter uncertainty. Results: We found that the RHP was dominant—cost-saving and more effective—compared to usual care. The RHP was 783USD cheaper than the standard of care and created 0.04 additional QALYs, per person. The Incremental Cost-Effectiveness Ratio (ICER) showed a cost per QALY gained of $21,660USD. In the PSA the RHP was dominant in 996 out of 1000 evaluated scenarios. Conclusions: The RHP was cheaper than the standard of care and more effective due to a reduction in the incidence of patients progressing to dialysis, which is a very expensive treatment and many times inaccessible. We aim these results to help in the decision-making process of scaling-up and investment of similar strategies in Peru. Our results help to increase the evidence in Latin America where there is a lack of information in the long-term consequences of clinical-management-based prevention strategies for CKD patients.