Flame of Recca follows the story of a teenage boy named Recca Hanabishi, who is interested in ninja and claims to be one himself. He often gets into fights because he made it publicly known that the person who manages to defeat him will earn his services as a loyal ninja. Despite this, he eventually pledges his loyalty and services as a ninja to Yanagi Sakoshita, a girl with the innate ability to heal any wound/injury, because of her kindness and compassion. Recca soon discovers that he possesses the innate ability to control/manipulate flames, and eventually learns that he is actually the son of the sixth generation leader of the Hokage, a ninja clan that was wiped out by Oda Nobunaga in 1576, roughly 400 years before the series' present day.
The Hokage ninjas wielded mystical objects called madōgu (魔導具?), which are referred to as "psychic devices" or "elemental weapons" in the English versions of the series. Madōgu grant their users special abilities, such as allowing their users to manipulate certain elements (as in the case of the Fūjin, which allows its wielder to manipulate the element of wind) and enhancing their user's strength/skills (as in the case of the Dosei no Wa, which increases its user's physical strength and the Idaten, which increases its user's running speed). Oda Nobunaga had invaded the Hokage in 1576 for the purpose of acquiring these weapons, and the series' main antagonist, Kōran Mori, is searching for a madōgu that will grant him eternal life. Recca and his friends become entangled in Mori's quest for eternal life as he initially attempts to kidnap Yanagi, believing that her healing powers will help him achieve immortality. This leads them to join the Ura Butō Satsujin, a tournament wherein the warriors that wield madōgu gather to battle each other. After successfully winning the tournament, Recca and his teammates discover that Mori was on his way to acquire the Tendō Jigoku (天堂地獄, Heaven and Hell?), a madōgu said to grant its user eternal life, and once again attempt to stop him.
Though initially following the same basic storyline, the Flame of Recca anime series ends right after the Ura Butō Satsujin ends, while the manga goes on to include the subplot involving the Tendō Jigoku. The anime also omits certain characters from the story, and several of the characters' physical appearances are slightly different from the manga.