After preparation at the Railway Technical Research Institute (RTRI) in Kokubunji, Tokyo, the train was moved to JR West tracks in January 1999 for testing on the Sanin Line at speeds of up to 100 km/h (62 mph).

From April 1999, the train was shipped to the Transportation Technology Center in Pueblo, Colorado, United States for an extended period of high-speed endurance running until January 2001.

[4] A series of 15 return test runs were conducted late at night between 23 August and 27 October 2004, starting at a maximum speed of 70 km/h (45 mph) on the first day.

[11] In 2011, the train was fitted with new lighter weight "E" bogies to improve stability and ride comfort when negotiating curves or points with radii of less than 600 m (1,969 ft).

[12] Endurance testing was then undertaken from December 2011 until September 2013 on the Yosan Line between Tadotsu and Matsuyama, during which time it covered a distance of approximately 70,000 km (43,496 mi).

[13][14] Following withdrawal of the set, one end car, GCT01-201, was moved from Tadotsu to Iyo-Saijo in July 2014 for display at the Shikoku Railway Heritage Museum in Saijō, Ehime.

[15] A third-generation, four-car, train was delivered to Kumamoto Depot in Kyushu in late March 2014,[16] and "three-mode" (standard-gauge - gauge-changing - narrow gauge) endurance testing using a new facility built near Shin-Yatsushiro Station commenced in October 2014.

[17] Testing was suspended in December 2014 after accumulating approximating 33,000 km (20,505 mi), following the discovery of defective thrust bearing oil seals on the bogies.

[19] In June 2017, JR Kyushu revealed that it had abandoned plans to use the GCT on the Nagasaki Shinkansen (opened in 2022) citing reasons of cost and safety.