X was originally pitched under the name Eclipse and was developed under the title Lunar Chase. The single-letter rename came at the request of Nintendo president Hiroshi Yamauchi, who contacted director Yoshio Sakamoto early in the morning after playing the game.

The Lunar Chase name was retained for a planned English localization of the game, which was ultimately scrapped due to fears from Nintendo of America that international players would find the game's presentation and design too complex for a handheld title. Creator and programmer Dylan Cuthbert additionally blamed the cancellation on a presumed lack of interest from retailers in the United States. A prototype of the English version would eventually surface in 2020 as part of the Gigaleak, a massive leak of internal server data from Nintendo. The Eclipse pitch, meanwhile, was released to the public by the Video Game History foundation three years later.

In a 2000 interview with the game's director Yoshio Sakamoto published in the Nice Games' Game Boy Navigator tankobon, he stated at the time, he had been developing Kaeru no Tame ni Kane wa Naru and 3D games were just beginning to emerge. Argonaut Software, an overseas company with a high degree of technical expertise, approached him and his team with the offer to make a 3D game with them. Sakamoto thought it would be a useful experience, so he took the job, but he noted it was hard, summing up the hardships he faced working on the game as "brutal". Sakamoto had not finished writing the scenario for Kaeru, so someone else was put in charge of his half-written scenario, and he told them to continue working on it until he returned. When the development of X was finished and he returned to see how Kaeru was turning out, the game was essentially content-complete, with the only thing left for him to do was to fine-tune the enemy placement and the balance of the maps himself. Despite his minimal involvement with that game, he thought that it turned out exactly as he imagined.

Nintendo fans generally acknowledge X to be the first game to implement "Totaka's Song," a 13-note melody composed by Nintendo music veteran Kazumi Totaka.

Totaka often implemented this melody for games he worked on, including Luigi's Mansion, The Legend of Zelda: Link's Awakening, and the Animal Crossing franchise.

Developer Dylan Cuthbert, who would later go on to create the original Star Fox for the SNES, said Argonaut wanted to create a 3D engine which, in turn, would help make a 3D game for the Game Boy. After presenting it to Nintendo, who were stunned by the fantastic design of the game, Nintendo purchased the rights to and released X, a Japan-only game.