The park was originally established in 1921 as the Mount Banahao Forest Reserve covering an area of . It was established through Proclamation No. 42 signed by Governor-General Leonard Wood for the reforestation, conservation and water protection of the area comprising mounts Banahao and San Cristobal. In 1941, President Manuel Luis Quezon signed Proclamation No. 716 reducing its size to divided into two parcels and declaring it a national park. Amendments to its area were made in 1961 and again, in 1966. In 2003, the Mounts Banahaw-San Cristobal National Park was reclassified as a protected landscape under the National Integrated Protected Areas System with the issuance of Proclamation No. 411 by President Gloria Arroyo.