The word putumayo comes from the Quechua languages. The verb p'utuy means "to spring forth" or "to burst out", and mayu means river. Thus it means "gushing river".
Originally, the southwestern area of the department belonged to the Cofán Indians, the northwestern to the Kamentxá Indians, the central and southern areas to tribes that spoke Tukano languages (such as the Siona), and the eastern to tribes that spoke Witoto languages. Part of the Kamentxá territory was conquered by the Inca Huayna Cápac in 1492, who, after crossing the Cofán territory, established a Quechua population on the valley of Sibundoy, known today as Ingas. After the Inca defeat in 1533, the region was invaded by the Spanish in 1542, and from 1547 was administered by Catholic missions.
The current territory of Putumayo was linked to Popayan during the Spanish Colonial Period and in the first Republican decades belonged to the "Azuay Department", which included territories in Ecuador and Perú. Later a long process of territorial redistributions began:
^Kline, Harvey F. (2012). "Putumayo, Department of". Historical Dictionary of Colombia. Lanham, Maryland: Scarecrow Press. p. 415. ISBN978-0-8108-7813-6.
^"DANE". Archived from the original on 13 November 2009. Retrieved 13 February 2013.
^"Reloj de Población". DANE. Departamento Administrativo Nacional de Estadísitica. Archived from the original on 28 October 2016. Retrieved 6 July 2017.