(Dates in italics indicate de facto continuation of office)
| Term | Incumbent | Notes |
|---|---|---|
| Portuguese Timor | ||
| Subordinated to Portuguese India | ||
| 1647 to 1649 | António de São Jacinto, Captain | In Cupão |
| 1649 to 1652 | Francisco Carneiro, Captain | In Cupão |
| 1652 to 1662 | ..., Captain | |
| 1662 to 1664 | Simão Luís, Captain | |
| 1665 to 1666 | Simão Luís, Captain-Major | |
| 1666 to 1669 | António Hornay, acting Captain-Major | 1st time |
| 1669 to 1670 | Fernão Martins da Ponte, acting Captain-Major | |
| 1671 to 1673 | Mateus da Costa, acting Captain-Major | |
| 1673 to 1693 | António Hornay, acting Captain-Major | 2nd time |
| 1680 | João Antunes Portugal, Captain-Major | Sent by Portugal but refused by settlers |
| 1694 to 1696 | Francisco Hornay, acting Captain-Major | |
| 1696 to 1697 | António de Mesquita Pimentel, Captain-Major | |
| 1697 | André Coelho Vieira, Captain-Major | |
| 1697 to 1702 | Domingos da Costa, acting Captain-Major | |
| 20 February 1702 to 1705 | António Coelho Guerreiro, Governor | |
| 1705 to 1706 | Lourenço Lopes, Governor | |
| 1706 to 1708 | Manuel Ferreira de Almeida, Governor | 1st time |
| 1708 to 1709 | Jácome de Morais Sarmento, Governor | |
| 1709 to 1714 | Manuel de Souto-Maior, Governor | |
| 1714 | Manuel Ferreira de Almeida, Governor | 2nd time |
| 1714 to 1718 | Domingos da Costa, Governor | |
| 1718 to 1719 | Francisco de Melo e Castro, Governor | |
| 1719 to 1722 | Manuel de Santo António, Governor | |
| 1722 to 1725 | António de Albuquerque Coelho, Governor | |
| 1725 to 1729 | António Moniz de Macedo, Governor | 1st time |
| 1729 to 1731 | Pedro de Melo, Governor | |
| 1731 to 1734 | Pedro do Rego Barreto da Gama e Castro, Governor | |
| 1734 to 1739 | António Moniz de Macedo, Governor | 2nd time |
| 1739 to 1741 | ..., acting Governor | |
| 1741 to 1745 | Manuel Leonís de Castro, Governor | |
| 1745 to 1748 | Francisco Xavier Moraes Doutel, Governor | |
| 1748 to 1751 | Manuel Correia de Lacerda, Governor | |
| 1751 to 1759 | Manuel Doutel de Figueiredo Sarmento, Governor | |
| 1759 to 1760 | Sebastião de Azevedo e Brito, Governor | |
| 1760 to 1763 | ..., acting Governor | |
| 1763 to 1765 | Dionísio Gonçalves Rebelo Galvão, Governor | |
| 1765 to 1768 | ..., acting Governor | |
| 1768 to 1776 | António José Teles de Meneses, Governor | |
| 1776 to 1779 | Caetano de Lemos Telo de Meneses, Governor | |
| 1779 to 1782 | Lourenço de Brito Correia, Governor | |
| 1782 to 1785 | João Anselmo de Almeida Soares, Governor | |
| 1785 to 1788 | João Baptista Vieira Godinho, Governor | |
| 1788 to 1790 | Feliciano António Nogueira Lisboa, Governor | |
| 1790 to 1794 | Joaquim Xavier de Morias Sarmento, Governor | |
| 1794 to 1800 | João Baptista Verquaim, Governor | |
| 1800 to 1804 | José Joaquim de Sousa, Governor | |
| 1804 to 1807 | João Vicente Soares da Veiga, Governor | |
| 1807 to 1810 | António de Mendonça Côrte-Real, Governor | |
| 1810 | António Botelho Homem Bernardes Pessõa, Governor | |
| 1810 to 1812 | Joaquim António Duarte da Silva Veloso, Governor | |
| 1812 to 1815 | Vitorino Freire da Cunha Gusmão, Governor | |
| 1815 to 1819 | José Pinto Alcoforado de Azevedo e Sousa, Governor | |
| 1819 to 1821 | Gregório Rodrigues Pereira, Governor | |
| 1821 to 1832 | Manuel Joaquim de Matos e Góis, Governor | |
| 1832 | Miguel da Silveira Lorena, Governor | |
| 1832 to 1834 | Miguel Carlos da Cunha da Silveira e Lorena, Governor | |
| 1834 to 1839 | José Maria Marques, Governor | |
| 1839 to 1844 | Frederico Leão Cabreira de Brito Alvelos Drago Valente, Governor | |
| Subordinated to Macau | ||
| 1844 to 1848 | Julião José da Silva Vieiras, Governor | |
| 1848 to 30 October 1850 | António Olavo Monteiro Torres, Governor | |
| Separate colony | ||
| 30 October 1850 to 1851 | António Olavo Monteiro Torres, Governor | |
| 23 June 1851 to 15 September 1851 | José Joaquim Lopes de Lima, Governor | |
| Subordinated to Macau | ||
| 15 September 1851 to 1852 | José Joaquim Lopes de Lima, Governor | |
| 1852 to 1856 | Manuel de Saldanha da Gama, Governor | |
| Subordinated to Portuguese India | ||
| 1856 to 1859 | Manuel de Saldanha da Gama, Governor | |
| 1859 to 1863 | Afonso de Castro, Governor | |
| Separate overseas province | ||
| 1863 to 1864 | José Manuel Pereira de Almeida, Governor | |
| 1864 to 1866 | José Eduardo da Costa Meneses, Governor | |
| Subordinated to Macau | ||
| 1866 to 1869 | Francisco Teixeira da Silva + António Joaquim Garcia, Governors | |
| 1870 to 1871 | João Clímaco de Carvalho + Manuel de Castro Sampaio, Governors | |
| 1873 to 1876 | Hugo Goodair de Lacerda Castelo Branco, Governor | 1st time |
| 1876 to 1878 | 'Joaquim António da Silva Ferrão + José Alves da Costa, Governors | |
| 1878 to 1880 | Hugo Goodair de Lacerda Castelo Branco, Governor | 2nd time |
| 1880 to 1881 | Augusto César Cardoso de Carvalho + José dos Santos Vaquinhas, Governors | |
| 1882 to 1883 | Bento da França Pinto de Oliveira + Porfírio Zeferino de Sousa + Francisco de Paula da Lua, Governors | 1st time for Porfírio Zeferino de Sousa |
| 1883 to 1885 | João Maria Pereira + Cipriano Forjaz, Governors | 1st time for Cipriano Forjaz |
| 1885 to 3 March 1887 | Alfredo de Lacerda Maia | |
| 1887 | António Joaquim Garcia, Governors | |
| 1887 to 1888 | António Francisco da Costa, Governor | |
| 1888 to 1889 | Rafael Jácome Lopes de Andrade, Governor | |
| 1889 to 1890 | Porfírio Zeferino de Sousa, Governor | 2nd time |
| 1890 to 1894 | Cipriano Forjaz, Governor | 2nd time |
| 1894 | Porfírio Zeferino de Sousa, Governor | 3rd time |
| 1894 to 15 October 1896 | José Celestino da Silva, Governor | |
| Separate colony | ||
| 15 October 1896 to 1908 | José Celestino da Silva, Governor | |
| 1908 | Jaime Augusto Vieira da Rocha, acting Governor | |
| 1908 to 1909 | Eduardo Augusto Marquês, Governor | |
| 1909 to 1910 | Gonçalo Pereira Pimenta de Castro, Governor | 1st time |
| 1910 to 30 October 1910 | Alfredo Augusto de Soveral Martins, Governor | |
| 1910 | Anselmo Augusto Coelho de Carvalho, acting Governor | |
| 1910 | José Carrazeda Caldas Viana e Andrade, acting Governor | |
| 1911 to 1913 | Filomeno da Câmara Melo Cabral, Governor | 1st time |
| 1913 to 1914 | Gonçalo Pereira Pimenta de Castro, acting Governor | 2nd time |
| 1914 to 1917 | Filomeno da Cámara Melo Cabral, Governor | 2nd time |
| 1917 | César de Abreu + José Machado Duarte Júnior, acting Governors | |
| 1917 to 1919 | Luís Augusto de Oliveira Franco, acting Governor | 1st time |
| 1919 to 1920 | Manuel Paulo de Sousa Gentil, Governor | |
| 1920 to 1921 | Luís Augusto de Oliveira Franco, acting Governor | 2nd time |
| 1921 | José de Paiva Gomes, Governor | 1st time |
| 1921 | Humberto dos Santos Leitão, acting Governor | 1st time |
| 1921 to 1923 | José de Paiva Gomes, Governor | 2nd time |
| 1923 to 1924 | Humberto dos Santos Leitão, acting Governor | 2nd time |
| 1924 to 1926 | Raimundo Enes Meira, Governor | |
| 1926 to 1929 | Teófilo Duarte, Governor | |
| 1929 to 1930 | Cesário Augusto de Almeida Viana, Governor | |
| 1930 | Abel Teixeira da Costa Tavares, acting Governor | |
| 1930 to 1933 | Antonio Baptista Justo, Governor | |
| 1933 | José Luís Fontoura de Sequeira, acting Governor | |
| 1933 to 1936 | Raúl de Antas Manso Preto Mendes Cruz, Governor | |
| 1936 | Eduardo Bernardo Lápido Loureiro, acting Governor | |
| 1937 to 1940 | Álvaro Eugénio Neves da Fontoura, Governor | |
| 1940 | António Jacinto Magro, acting Governor | |
| 1940 to 8 December 1945 | Manuel de Abreu Ferreira de Carvalho, Governor | Considered himself a prisoner during allied rule from December 1941 until February 1942; confined by Japanese from February 1942 until August 1945 |
| Occupation of Portuguese Timor by Australian and Dutch forces | ||
| 17 December 1941 to 20 February 1942 | William Watt Leggatt, Commander of Australian forces | |
| 17 December 1941 to 20 February 1942 | Nico Leonard Willem van Straten, Commander of Dutch forces | |
| Occupation of Portuguese Timor by Japanese forces | ||
| 20 February 1942 to 1942 | Sadashichi Doi, Commander | |
| August 1942 to November 1944 | Yuichi Tsuchihashi, Commander | |
| November 1944 to August 1945 | Kunitaro Yamada, Commander | |
| Portuguese Timor | ||
| 1946 to 1950 | Óscar Freire de Vasconcelos Ruas, Governor | |
| 1950 to 11 June 1950 | César Maria de Serpa Rosa, Governor | |
| Overseas province | ||
| 11 June 1950 to 1958 | César Maria de Serpa Rosa, Governor | |
| 1959 to 1963 | Filipe José Freire Temudo Barata, Governor | |
| 1963 to 1968 | José Alberty Correia, Governor | |
| 1968 to 1972 | José Nogueira Valente Pires, Governor | |
| 1972 to 1974 | Fernando Alves Adeía, Governor | |
| 18 November 1974 to 27 November 1975 | Mário Lemos Pires, Governor | |
| 28 November 1975 | Unilateral declaration of independence as Democratic Republic of East Timor | |
| 7 December 1975 | Invaded by Indonesia | |
| 17 July 1976 - 19 October 1999 | Annexed by Indonesia (Timor Timur province). Not recognized by Portugal; remained recognized by United Nations as Portuguese territory. | |
| 30 August 1999 | Referendum votes for independence 78% | |
| 20 September 1999 - 19 May 2002 | International administration (from 28 February 2000, under UN administration; United Nations Transitional Administration in East Timor [UNTAET]). | |
| 20 May 2002 | Independence as Democratic Republic of East Timor | |
For continuation after independence, see: President of East Timor