Agusan derived its name from the local dialect, agasan, meaning "where the water flows", referring to the Agusan River that splits the land and meanders south to north in a 250-kilometre (160 mi) rush to Butuan Bay. It is third largest river in the country and served as highway for the Spanish colonizers in gaining access to inner northeastern Mindanao.

The Agusan Valley was settled by a variety of cultural communities like the Manobos, Mamanwas and Higaonons. Archeological excavations in the lower Agusan valley plains have uncovered evidence of strong relationships between the region and the Southeast Asian states. A golden image of Javan-Indian design unearthed in the 1920s and molten jars uncovered in Prosperidad are indications that the region had commercial and cultural ties with the coast.

The Augustinian Recollects established a mission in Linao, in the vicinity of present-day Bunawan, in 1614. However, mission work was hampered by the hostility of the surrounding Manobo tribes. At the height of the power of the Sultanate of Maguindanao in the mid-17th century, the Manobos of the Agusan Valley were in alliance with Sultan Kudarat. Linao was attacked several times during the 1629 Caraga Revolt and the 1649 Sumuroy Revolt. Nevertheless, the Recollects were able to establish themselves in their mission work, and remained there until the middle of the 19th century.

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