Panyagor is commonly said to have once been a 'wut' (cattle camp) belonging to the Ayual community.

[3] Joseph Oduho, a founding member of the Sudan People's Liberation Movement (SPLM), was killed in Payagor on 27 March 1993.

He had traveled there to discuss how to build a new coalition after the violent breakup of the Sudan People's Liberation Army (SPLA) into rival factions.

[4][5] A cargo plane chartered by Norwegian Church Aid and carrying material for a Lutheran World Federation WASH (water, sanitation and hygiene) project in Jonglei crashed in Panyagor on 14 November 2014.

[6][7][8] During the floods of 2013, which displaced many people and destroyed homes in Panyagor, parts of the town were overrun by hippopotamuses looking for pasture.