Antimicrobial prophylaxis and treatment of opportunistic infections immediately before or at the start of antiretroviral therapy (ART) improves prognosis and decreases death rates among patients with advanced HIV disease (AHD). In this study, we estimated the average cost per patient receiving AHD services (PP) and per client retained (PR) at 12 months. The study population included children, adolescents, and adults enrolled in the AHD program at 13 hub and 19 spoke sites in Malawi. To evaluate the cost PP and PR, we divided the cost of providing AHD services at 12 months by the total number of patients who received these services and who were retained in AHD services care at 12 months, respectively. We enrolled 246 AHD patients, with 137 retained at 12 months. The cost of providing AHD services to 246 patients at 12 months was $59,063; cost PP was $240, and cost PR was $431. Drugs were the largest expenditure (30%), followed by travel for supportive supervision (24%), clinic visit costs (19%), site support personnel (8%), laboratory tests (7%), annualized training costs (6%), consumables (3%), and meetings (3%). The cost of ART was $11,754; however, ART would be provided regardless of whether the AHD package was in place. Any reduction in overall costs of AHD care will require coordination among procurement partners and negotiations with manufacturers to help reduce the prices of drugs and laboratory consumables. This calls for further improvement of efficiency and capacity of site-level staff to reduce costs related to supportive supervision.