To achieve its statutory objectives, the Bank of Botswana is guided by its vision and mission, and decisions of the Board. Effective January 1, 2023, the Bank adopted a new organisational structure, which shows an increase in the number of functional Departments from eleven (11) and one Division to thirteen (13) Departments, one Division, and a semi-autonomous Deposit Insurance Scheme, as articulated in the Bank of Botswana (Amendment) Act, 2022. All Departments and the Division report to the Governor through the Chief Operating Officer/General Counsel and Deputy Governors.

The Governor, Deputy Governors, Chief Operating Officer, General Counsel and Heads of Department, as well as senior advisors who may be co-opted, comprise the Bank's Executive Committee. This meets fortnightly and is chaired by the Governor. The work of the Bank is further coordinated by various committees.