It occupies the far western end of Timor Island (apart from the area of Kupang city, which has been administratively separated from the Regency since 11 April 1996), together with the smaller island of Semau (off the southwestern tip of Timor) and other minor offshore islands (of which Kera is the only inhabited).

Other islands further to the southwest and west which were formerly part of Kupang Regency have been separated administratively - the Rote Islands Group on 10 April 2002 (to form Rote Ndao Regency), and the Savu Islands Group on 29 October 2008 (to form Sabu Raijua Regency).

The residual regency covers an area of 5,668.26 square kilometres (2,188.53 sq mi).

[2] The regency is divided into twenty-four districts (kecamatan), tabulated below with their areas and their populations at the 2010 Census[3] and the 2020 Census,[4] together with the official estimates as at mid 2023.

The table also includes the locations of the district administrative centres, the number of administrative villages in each district (totaling 160 rural desa and 17 urban kelurahan), and its post code.