As created, Jayawijaya Regency covered an area coincident with the whole of what in 2022 became Highland Papua Province. However, on 11 December 2002 three new Regencies - Bintang Mountains Regency (Kabupaten Pegunungan Bintang), Tolikara Regency, and Yahukimo Regency - were created from parts of Jayawijaya Regency. Subsequently on 4 January 2008 another four new Regencies - Lanny Jaya Regency, Central Mamberamo Regency (Kabupaten Mamberamo Tengah), Nduga Regency, and Yalimo Regency - were created from further parts of Jayawijaya Regency. All eight regencies were brought together again in 2022 in the new province of Highland Papua.

At the time of the 2010 Census, the Jayawijaya Regency comprised eleven districts (distrik), listed below with their populations at the 2010 Census. During the following ten years, the number of districts was raised to forty by the splitting of existing districts, and these are all shown below with their current areas and their populations at the 2010 Census^[2] and the 2020 Census,^[3] together with the official estimates as at mid-2022.^[1] The table also includes the locations of the district administrative centres, the number of administrative villages in each district (totaling 328 rural kampung and 4 urban kelurahan), and its postcode.

Notes: (a) including the three kelurahan of Wamena Kota (Wamena town), Sinakma and Sinapuk. (b) including the kelurahan of Ilokama.

Note that those districts with 2010 populations given in the 2010 Population column (and numbered from 95.01.01 to 95.01.11) were the eleven districts extent in 2010; the remaining twenty-nine districts with no figure given in the 2010 Population column (and numbered from 95.01.12 to 95.01.40) were those created from the original eleven districts subsequent to 2010.

• Statistics publications from Statistics Indonesia (BPS)