| No. | Name | From | To | Head of State | Notes |
| - | G Oda | 1960 | 1962 | Benedicto Kiwanuka | Oda was minister under Prime Minister Benedicto Kiwanuka and the first to take the title of minister and not secretary. He was Minister of Internal Affairs under the transitional government. |
| 1 | Cuthbert Joseph Obwangor | 1962 | 1964 | Apollo Milton Obote | Obwangor was Minister of Regional Administration which briefly assumed the responsibilities of the Ministry of Internal Affairs. |
| 1 | Felix Kenyi Onama | 1962 | 1964 | Apollo Milton Obote | Onama also can lay claim to the Minister of Interior position between 1962 and 1964, as he was Minister of Works and Labour. That role assumed some of the other responsibilities of the Minister of Interior like leading the police. |
| 2 | Basil Kiiza Bataringaya | 1964 | 1971 | Apollo Milton Obote | Basil Kiiza Bataringaya headed the newly created Ministry of Home Affairs, later renamed Ministry of Internal Affairs. He assumed the role after he flipped parties and joined the Obote administration. |
| 3 | Lt. Col. Ernest Obitre Gama | 1971 | 1973 | Idi Amin | |
| 4 | Charles Oboth‐Ofumbi | 1973 | 16 February 1977 | Idi Amin | |
| 5 | Paulo Muwanga | 1978 | 1980 | Yusuf Lule | |
| 5 | Paulo Muwanga | 1978 | 1980 | Godfrey Binaisa | |
| 5 | Paulo Muwanga | 1978 | 1980 | Presidential Commission of Uganda | |
| 5 | Paulo Muwanga | 1978 | 1980 | Paulo Muwanga | Paulo Muwanga became head of state briefly when the Presidential Commission of Uganda gave him the powers of the President of Uganda from 22 May to 15 December 1980, where he also was Minister of Internal Affairs. |
| 6 | John Mikloth Magoola Luwuliza-Kirunda | 1981 | 1985 | Apolo Milton Obote | Dr. John M. M. Luwuliza Kirunda left the role when he became Foreign Minister |
| 7 | Paul Ssemogerere | 1985 | 1988 | General Bazilio Olara-Okello | Paul Ssemogerere left the position when he became Foreign minister |
| 7 | Paul Ssemogerere | 1985 | 1988 | General Tito Okello | Paul Ssemogerere left the position when he became Foreign minister |
| 7 | Paul Ssemogerere | 1985 | 1988 | Yoweri Museveni | Paul Ssemogerere left the position when he became Foreign minister |
| 7 | Paul Ssemogerere | 1985 | 1988 | Yoweri Museveni | Paul Ssemogerere stayed on for the beginning of Yoweri Museveni's administration. |
| 8 | Kahinda Otafiire | 1988 | 1989 | Yoweri Museveni | Maj. Kahinda Otafiire had to resign as Minister of Internal Affairs after he brandished a pistol at a woman at a Kampala bar. |
| 9 | Ibrahim Mukiibi | 1989 | 1994 | Yoweri Museveni | |
| 10 | Crispus Kiyonga | 1994 | 1996 | Yoweri Museveni | |
| 11 | Eriya Kategaya | 1996 | 2001 | Yoweri Museveni | |
| 12 | James Wapakhabulo | 2001 | 2004 | Yoweri Museveni | Died in office |
| 13 | Tom Butime | 2004 | 2005 | Yoweri Museveni | In acting capacity |
| 14 | Hilary Onek | 27 May 2011 | 23 May 2013 | Yoweri Museveni | |
| 15 | Aronda Nyakairima | 23 May 2013 | 12 September 2015 | Yoweri Museveni | |
| 16 | Rose Akol | 13 November 2015 | 6 June 2016 | Yoweri Museveni | |
| 17 | Jeje Odongo | 6 June 2016 | Present | Yoweri Museveni | |
