Unlike many other cultural groups in what is now Peru, the Aguaruna were never successfully conquered by the Inca, although there are accounts of attempts to extend into the territory by Incas Huayna Capac and Tupac Inca Yupanqui.
The Spanish conquistadors first encountered the Aguaruna in 1549 when the towns of Jaén de Bracamoros and Santa Maria de Nieva were founded.