The Uchiha clan was descended from the elder of the two boys entrusted by the Sage of the Six Paths with the power and will of the way of the ninja. The elder believed that might would bring peace. The Sage chose the younger as more fitting to be his successor, causing the elder to be vengeful. From the younger boy descended the Senju clan who would be the eternal rivals of the Uchiha.

Before the founding of the ninja villages, the Uchiha were one of the many mercenary clans for hire. Because of their Sharingan, the Uchiha clan came to be known as one of the two strongest clans, the second being the Senju clan. Madara Uchiha was particularly powerful, and, upon attaining the Mangekyo Sharingan, he took control of the clan. Under his leadership the Uchiha grew stronger, conquering whatever clans they came upon, such that, whenever the Uchiha clan was hired for a job, the opposing side would hire the Senju.

Hashirama Senju, the leader of the Senju clan, grew tired of the endless fighting, and approached the Uchiha clan with a peace treaty. Madara feared that an alliance would lead the Uchiha to ruin, but his clan disagreed, and he was forced to accept. The two clans came together to form Konoha, with Hashirama being selected as Hokage. Madara believed that this was proof that the Uchiha would be made subservient to the Senju, but his clan saw this only as his attempt to rekindle the flames of war. They turned their backs on him, and he defected. Following Madara's betrayal, the Second Hokage gave the Uchiha control of the Konoha Military Police as a sign of trust. According to Madara, this was really just a way of keeping the Uchiha in check and out of Konoha's governing affairs.

The Uchiha clan after the founding of Konoha.

Decades later, after the Demon Fox Attack of Konoha, Konoha began to suspect that an Uchiha was behind the attack. The Uchiha were relocated to a corner of the village so that they could be more easily monitored. The Uchiha interpreted this as confirmation of what Madara had warned them of years earlier, and began to plan overthrowing the village. One Uchiha, Itachi, disagreed with the coup d'état, and informed Konoha's leadership of what the Uchiha were up to. To prevent an uprising that would create another war, Itachi was ordered to wipe out the Uchiha.

Itachi spared only one Uchiha: his younger brother, Sasuke. Sasuke would spend the next few years trying to avenge their family by killing Itachi, something Itachi had planned for from the very beginning. Once accomplishing this goal, Sasuke learned that Madara was also still alive. Madara told Sasuke about the Uchiha's history and why Itachi had wiped out the Uchiha, prompting Sasuke, with Madara's help, to resolve to destroy Konoha.