Kaito Kuroba is a seventeen-year-old high school student who is an adept magician due to the influence of his father, Toichi Kuroba. Eight years prior to the series, Toichi had mysteriously died and was also the last time the Phantom Thief Kid was spotted. In the present time, Kaito discovers a secret room in his home that was set up by his father to reveal itself on that very day. Finding the Phantom Thief Kid's gadgets and costume in the room, Kaito dons the disguise and decides to confront Kid who has recently revealed himself after his eight years of absence. Kaito discovers Kid to be Konosuke Jii (寺井 黄之助 Jii Kounosuke), his father's butler, who reveals Toichi was indeed the first Phantom Thief Kid. Jii reveals his took on the role as Kid to lure out Toichi's murderer. Upon learning that his father was murdered, Kaito continues to play the role of the Phantom Thief Kid as he searches for his father's killer.

As the Phantom Thief Kid, Kaito uses his skills of perfect disguise and the gadgets his father left him to complete his heists. The most prominent of those gadgets are his cape which transforms into a hang-glider, a gun that shoots sharp metallic playing cards, and smoke bombs. To lure out the murderers, Kaito adopts a tradition of sending a note of his intending theft to the location beforehand. After a successful heist, Kaito either return the stolen treasures or throws them away. As the Phantom Thief Kid, Kaito eventually meets the organization who killed his father. He discovers they are searching for the jewel called Pandora (パンドラ) which grants immortality if the water it emits during Volley's Comet is drank. Pandora is hidden in a larger jewel and can only be seen if shone under the moonlight. Kaito decides to search for Pandora with the intention of destroying it and begins focusing his heists on large jewels. As such, he begins the tradition of checking jewels from his heists under the moonlight before returning them to their rightful owners.