The Park was established on March 26, 1971, by virtue of Proclamation No. 835 issued by the late President Ferdinand E. Marcos. Formerly known as the St. Paul Subterranean National Park, it comprised of 3,901 hectares of terrestrial reservation. Experts later concluded that the size of the Park was inadequate to protect the water shed of the Underground River and the significant biodiversity present. To ensure long-term viability, Proclamation No. 212 was signed by President Joseph E. Estrada on November 16, 1999 expanding its area to 22,202 hectares that now includes the entire catchment for the Underground River and the forest ecosystems important for biodiversity conservation. It was also renamed to Puerto Princesa Subterranean River National Park to properly identifying it with the place.

The PPUR officially represented the Philippines in the global search for the New 7 Wonders of Nature. Pres. Benigno S. Aquino signed proclamation No. 182 on June 3, 2011 declaring a national and international campaign for the PPUR. This united Filipinos here and abroad who solidly supported the campaign and voted for inclusion of the Philippines to ssuch a prestigious list. The PPUR was declared as one of the New 7 Wonders of Nature on November 11, 2011.