IHI is registered in Tanzania as a Trust (registration 1487, 24 July1996). IHI's supreme Board of Governors (BOG) is chaired by the Director General of COSTECH and includes representatives from Ministry of Health and Social Welfare, National Institute for Medical Research, Swiss TPH, Swiss Agency for Development and Cooperation and Nelson Mandela AIST. The Board of Trustees (BOT) comprises the same membership, plus members of IHI's Management Committee. 

The BOG and BOT meet quarterly. Annual audited accounts and annual budgets are scrutinised by the BOT for formal final approval by the BOG. Both Boards are also responsible for approval of administrative regulations, financial procedures and scheme of service. 

IHI's executive is led by the Chief Executive Director (Dr. Salim Abdulla), assisted by the Deputy Chief Executive Director (Dr. Godfrey Mbaruku). Other Director-level positions include Director of Training (Dr. Rose Nathan), Director of Research (Dr. Honorati. Masanja), Director of Finance and Administration (Mr. Barnabas Lugendo), Director of Operations (Mr. Bakari Bakari) and Director of Knowledge Synthesis & Communication (under recruitment). The Branch leaders also form a part of the "Directorate" 

Three internal standing committees help to discharge routine business and support decision-making. These are the Management Committee, the Training Committee and the Scientific Committee. In addition, IHI has an Internal Review Board which is responsible for ethical scrutiny of new research proposals and onward submission for ethical approval by national authorities.