Background: A cost analysis of implementation of interventions informs budgeting and economic evaluations. Objective: To estimate the cost of implementing the integrated chronic disease management (ICDM) model in primary healthcare (PHC) clinics in South Africa. Methods: Cost data from the provider’s perspective were collected in 2019 from four PHC clinics with comparable patient caseloads (except for one). We estimated the costs of implementing the ICDM model current activities for three (facility reorganization, clinical supportive management and assisted self-management) components and additional costs of implementing with enhanced fidelity. Costs were estimated based on budget reviews, interviews with management teams, and other published data. The standard of care activities such as medication were not included in the costing. One-way sensitivity analyses were carried out for key parameters by varying patient caseloads, required infrastructure and staff. Annual ICDM model implementation costs per PHC clinic and per patient per visit are presented in 2019 US dollars. Results: The overall mean annual cost of implementing the ICDM model was $148 446.00 (SD: $65 125.00) per clinic. Current ICDM model activities cost accounted for 84% ($124 345.00) of the annual mean cost, while additional costs for higher fidelity were 16% ($24 102.00). The mean cost per patient per visit was $6.00 (SD:$0.77); $4.94 (SD:0.70) for current cost and $1.06 (SD:0.33) for additional cost to enhance ICDM model fidelity. For the additional cost, 49% was for facility reorganization, 31% for adherence clubs and 20% for training of nursing staff. In the sensitivity analyses, the major cost drivers were the proportion of effort of assisted self-management staff and the number of patients with chronic diseases receiving care at the clinic. Conclusion: Minimal additional cost are required to implement the ICDM model with higher fidelity. Further research on the cost-effectiveness of the ICDM model in middle-income countries is required.