It is likely that it was previously visited in 1522 by the Spanish sailor Gonzalo de Vigo, deserter from the Magellan expedition in 1521, and the first European castaway in the history of the Pacific.

[5] In 1914, during World War I, the island was captured by the Empire of Japan, which was awarded control by the League of Nations as part of the South Seas Mandate.

The island was settled by ethnic Japanese and Okinawans, who restored the coconut plantations and raised cotton and sweet potatoes for export.

In June 1944 a garrison force of 2,150 men of the Imperial Japanese Army arrived,[6] only to be cut off and isolated by the ongoing Allied offensive.

Receiving supplies only occasionally by submarine, the garrison soon faced starvation, and several hundred died of malnutrition before the surrender of Japan.

After World War II, Pagan was occupied by the United States as part of the UN Trust Territory of the Pacific Islands.

The US Navy maintained a small establishment on Pagan and during the 1950s built public institutions, including a church, a copra warehouse, an infirmary and a school house.

United States Air Force C-130 aircrew observed cattle and a small cluster of buildings, including a grass airstrip, located on the island.

Plans by a Japanese investor group to use Pagan as a dumping ground for debris and rubble from the 2011 Tōhoku earthquake and tsunami in Japan were provisionally shelved after protests in June 2012.

The southern volcano (18°04′30″N 145°43′30″E / 18.075°N 145.725°E / 18.075; 145.725), is 548 m (1,798 ft) high with a caldera approximately 4 km (2.5 mi) in diameter, consisting of four joined craters.

[13] In 2013 the US Naval Command filed a proposal to obtain the island for a new group of live-fire and maneuver Ranges and Training Areas (RTAs).

[17] On April 3, 2015 (HST) the Department of Defense (DoD) released a long-awaited draft of the Environmental Impact Statement (EIS).

[18] According to Michael G. Hadfield, a professor of biology at the University of Hawaiʻi at Mānoa who led an insect survey team to Pagan in 2010, "Speaking as a biologist, it's got some really unique things about it.

[17] According to an article by James Cave for the Huffington Post, an article which used Hadfield as its source: "More than 50 families in Saipan consider Pagan their home island and have plans and desires to return to homesteads," The island is occupied by two people, who live in shacks and have one flushing toilet and plumbing, electricity and small ranch.

In wording that hints at the hornet's nest the U.S. may have stirred with the proposal, the joint resolution asserts that "throughout the CNMI's history, foreign powers and outside influences have made major decisions and have dictated the course of development" for the region and that the U.S. "once again stands poised to make some very important decisions with respect to the military utilization of the Northern Islands."