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The office of the Auditor General has a very long history that can be traced to as far as back as 1900. From then up to 1920, the accounts of the Uganda Protectorate Government were audited by a team of auditors from the Director of Colonial audit in London. The Uganda Office was established in 1929 and was headed by Mr. R. H Carter at a rank of Auditor. In 1952 the Headquarters of the office moved to Kampala at the Treasury Building its current seat from Entebbe headed by Mr. Haywood as Auditor General.

The Office started by auditing the central Ministry accounts of the Protectorate Government. However, services were later extended to Buganda Kingdom funds including local authorities accounts. During the 1960s a number of public enterprises and corporations were created with requirements that the Auditor General audits their accounts. This has remained one of the key functions of the office.

By 1962, there were three regional offices namely; Entebbe Branch for central and Western regional, Mbale Branch for Eastern and North Eastern region and Gulu Branch for Northern and North Western region. More six branches were opened up in 1975 as the volume of work increased due to the creation of more administrative units. These were Jinja, Fortportal, Mbarara, Arua, Masaka and Soroti.

The Office of the Auditor General has had five Auditor Generals since independence. Mr. Night who was the last British Auditor General handed over to Mr. G.H. Kabiswa who was the first African Auditor General in 1968 and he served up to 1975 followed by Mr. Leo Outeke from 1975 to 1992, Mr. James Kahooza 1992 to 2001 who was followed by Mr. John F.S. Muwanga who is the current Auditor General.