(Dates in italics indicate de facto continuation of office)
| Tenure | Incumbent | Affiliation | Notes |
|---|---|---|---|
| Transkei (Self-Rule) | |||
| 6 December 1963 to 26 October 1976 | Kaiser Daliwonga Matanzima, Chief Minister | TNIP | |
| Republic of Transkei (Independent) | |||
| 26 October 1976 to 20 February 1979 | Kaiser Daliwonga Matanzima, Prime Minister | TNIP | Becoming President |
| 20 February 1979 to 24 September 1987 | George Mzivubu Matanzima, Prime Minister | TNIP | Resigned |
| 25 September 1987 to 5 October 1987 | Dumnisani Gladstone Gwadiso, Acting Prime Minister | TNIP | |
| 5 October 1987 to 30 December 1987 | Stella Sigcau, Prime Minister | TNIP | ♀; Deposed |
| 30 December 1987 to 26 April 1994 | Bantu Holomisa, Head of the Military Council | Mil | |
| Transkei re-integrated into South Africa on 27 April 1994 | |||