Background: Immunoglobulin (Ig) replacement therapy is used for treating a variety of primary immunodeficiency diseases (PIDs). Ig replacement therapy is the most important therapy for these diseases, since it protects the body against infections and reduces autoimmune disease symptoms. The purpose of this research was to estimate the cost of subcutaneous and intravenous Ig therapy in Iran. Methods: This study is carried out from the perspective of Iran's healthcare system and all the medical costs are calculated. Cost variables include personnel, equipment, and supplies. The data required for cost estimation are obtained from the records of children's Medical center of Tehran for 2015. Personnel and medical treatment costs are calculated based on relative value units. For SCIg, cost items are extracted from the literature. Results: The total cost of IVIg and SCIg for the health system in the first year of treatment is $1370 and $121 respectively. The results indicate that SCIg reduces costs and is the preferred treatment for PID patients. Conclusions: SCIg therapy significantly reduces the costs of the healthcare system compared to IVIg therapy, and this is enough economic justification for introduction of this treatment in the Iranian healthcare system. SCIg is also critical in reducing the direct costs of patients.