As a military base

The airfield was first developed by the Imperial Japanese Navy in 1937, with much of the land claimed from local farmers under the orders of Emperor Hirohito. Unlike many other Japanese military bases, it did not become a US base during the occupation. After the end of World War II, the locals reclaimed the land and resumed farming the land. The base was reopened in 1956 by the Japan Air Self-Defense Force, which took control of the land once again. Many farmers who live around the base have refused to sell their lands to the government to enable expansion of the airfield.

In September 1976 the MiG-25 Foxbat flown by the defecting Soviet pilot Victor Belenko to Hakodate Airport in Hokkaido was moved to Hyakuri by a US Air Force C-5 Galaxy. Despite strong Soviet protests, the Soviet aircraft was extensively examined and disassembled before being returned to the Soviet Union.

In February 1998 Chi Haotian, the-then Chinese defense minister, visited the base among other military sites in Japan.

In 2001 aircraft from Hyakuri were involved in intercepting Tupolev Tu-22M bombers of the Russian Air Force that had entered Japanese airspace.

In 2005 Japan and the US agreed to move some USAF F-15 fighter drills from Kadena Air Base in Okinawa to decrease the burden on that prefecture. Drills were to be moved to five other bases around the country - Chitose in Hokkaido, Hyakuri in Ibaraki Prefecture, Komatsu in Ishikawa Prefecture, Tsuiki in Fukuoka Prefecture and Nyutabaru in Miyazaki Prefecture. In 2005 USAF F-15 aircraft from Kadena Air Base in Okinawa deployed to the base as part of exercise Keen Sword 2005.

In April 2006 the Omitama city assembly unanimously opposed the F-15 training taking place at Hyakuri.

In May 2006 the US and Japan agreed to transfer part of the drills to the bases including Hyakuri with the US deploying to each base two or three times per year from 2007, with Japan footing 75% of the cost. US military personnel sometimes use the base for training or exchange programs. US Navy aircraft sometimes visit the base also, with F/A-18E Super Hornets of VFA-195 based at Naval Air Facility Atsugi in Kanagawa Prefecture deploying there briefly in 2016.

In January 2016 the JASDF used three Kawasaki T-4 trainers from the airport to collect radioactive material after North Korean's fourth nuclear test, which North Korea claimed was a hydrogen bomb test.

In October 2017 an F-4EJ Kai Phantom II of 302nd Tactical Fighter Squadron caught fire on the ground after its landing gear malfunctioned. There were no injuries.

Hyakuri Peace Park

The Hyakuri Peace Park is located in the air base. The main taxiway used by the air base goes around it.

Air Show

Hyakuri Air Base holds an annual air show in December featuring displays of military aircraft from the base as well as other equipment. There is a display by Blue Impulse, the JASDF aerobatic team.

As a civilian airport

In March 2010, after a 22 billion yen ($243 million) local and national government investment, the airfield was renamed to Ibaraki Airport, and civil aviation operations began. At the time of opening, Ibaraki offered two flights, an Asiana service to Seoul, South Korea, and to Kobe in western Japan, by Skymark Airlines. The original plans for a three-story terminal with separate arrivals, departures, and sightseeing levels was scrapped by the governor of Ibaraki Prefecture, Masaru Hashimoto, who ordered the building to be reduced to one story in height, to reduce costs. The airport will eschew jetways, with passengers boarding planes from the tarmac. Additional cost-cutting measures, intended to allow the airport to charge lower landing fees than those at Narita and Haneda, include the use of aircraft parking procedures that reduce or eliminate the need for pushback tractors, and the possibility of having the passengers carry their own luggage to the aircraft, a practice used at some regional airports in the United States.

Interest in the airport has been expressed by the Malaysian carrier AirAsia X as well as Korean airline Asiana, but only the latter has committed to flying out of the airport on a fixed basis. TransAsia Airways has committed to flights to and from Taipei's Taoyuan Airport on a semi-regular basis from March to May. During the May holiday, charters to Guam, Cebu, Bali, and Hainan will operate out of the airport. Also, China-based low-cost carrier Spring Airlines has chosen this airport as its Tokyo-area destination with its recent approval for international flying. It planned to run three charter flights a week from Shanghai-Pudong starting from about the end of July 2010 for about two months, switching to scheduled flights at the end of this period (around the end of the World Expo). However, it has started selling seats on the charters in the same manner as a normal flight since September 2010, much like the early Hongqiao-Haneda "scheduled charters" and has operated the flight as a scheduled service starting from 2011. In addition, it has now increased service to five flights a week.

As of March 2011, flights to Shanghai were operating at 80% capacity and the flights to Kobe at 50% capacity.