The Medical Stores Department (MSD) was established by the Act of Parliament No.13 of 1993 as an autonomous department under the Ministry of Health, responsible for developing, maintaining, and managing an efficient and cost-effective system of production, procurement, storage, and distribution of approved medicines and medical supplies required for use by all public health facilities.

The Board of Trustees is the highest decision-making body that governs and sets the direction of MSD on behalf of the Ministry of Health, . The Board comprises nine (9) members appointed every three years. The President of the United Republic of Tanzania appoints the Chairman while the Minister responsible for health appoints the rest (8) members. The Director General serves as the Secretary to the Board but has no right to vote.

To ensure the effective implementation of its responsibilities, the Board operates through three committees namely; Audit and Risk Management Committee, Technical Services Committee, and Finance and Administration Committee. The Board delegates the day-to-day management of the Department to the Director General who is appointed by the President of the United Republic of Tanzania.

The administrative functions and operations of the Department are carried out by and through the Executive Management Team (EMT). The EMT is constituted by the Director General, Director of Human Resources and Administration, Director of Finance, Director of Logistics, Director of Procurement, Director of Information and Communication Technology, Director of Customer Service and Zonal Operations. The Chief Legal Counsel serves as Secretary to the EMT.

The Medical Stores Department operates through ten zonal stores in Dar es Salaam, Mwanza, Iringa, Kilimanjaro, Mbeya, Tabora, Dodoma, Tanga, Mtwara, and Kagera.