In 1754, Governor-General Pedro Manuel de Arandía Santisteban sent Comandante Dovilla, who was based in Pangasinan, to establish a civil government and spread Christianity among the non-Christian Tribes.

The mission first saw the Valley of Yapa (Yapa meaning bountiful) which was inhabited by the Allagots, the second descendants of the Bormangi and Owak, and the third descendants of the Kalanguya, Ibaloi, Ilo-o, and Karao tribes who settled in the fertile valley.

In 1891, as part of a comprehensive plan to subdue the tribes of the Cordilleras, Governor-General Valeriano Weyler established the Comandancia Politico-Militar of Kayapa, which covered what would become the entire municipality, and placed a permanent military garrison there, which existed until their withdrawal during the Philippine Revolution.

Poverty incidence of Kayapa Source: Philippine Statistics Authority[12][13][14][15][16][17][18][19] Kayapa, belonging to the lone congressional district of the province of Nueva Vizcaya, is governed by a mayor designated as its local chief executive and by a municipal council as its legislative body in accordance with the Local Government Code.

The Schools Division of Nueva Vizcaya governs the town's public education system.