Cuauhtemoc's date of birth is unknown, as he does not enter the historical record until he became Emperor. He was the eldest legitimate son of Emperor Ahuitzotl and may well have attended the last New Fire ceremony, marking the beginning of a new 52-year cycle in the Aztec calendar. Like the rest of Cuauhtemoc's early biography, that is inferred from knowledge of his age, and the likely events and life path of someone of his rank. Following education in the calmecac, the school for elite boys, and then his military Service, he was named ruler of Tlatelolco, with the title cuauhtlatoani ("eagle ruler") in 1515. To have reached this position of rulership, Cuauhtemoc had to be a male of high birth and a warrior who had captured enemies for sacrifice.

When Cuauhtemoc was elected tlatoani in 1520, Tenochtitlan had already been rocked by the invasion of the Spanish and their indigenous allies, the death of Moctezuma II, and the death of Moctezuma's brother Cuitlahuac, who succeeded him as ruler, but died of smallpox shortly afterwards. In keeping with traditional practice, the most able candidate among the high noblemen was chosen by vote of the highest noblemen, Cuauhtemoc assumed the rulership. Although under Cuitlahuac Tenochtitlan began mounting a defense against the invaders, it was increasingly isolated militarily and largely faced the crisis alone, as the numbers of Spanish allies increased with the desertion of many polities previously under its control.

Cuauhtémoc called for reinforcements from the countryside to aid the defense of Tenochtitlán, after eighty days of warfare against the Spanish. Of all the Nahuas, only Tlatelolcas remained loyal, and the surviving Tenochcas looked for refuge in Tlatelolco, where even women took part in the battle. Cuauhtémoc was captured on August 13, 1521, while fleeing Tenochtitlán by crossing Lake Texcoco with his wife, family, and friends.

There are a number of discrepancies in the various accounts of the event. According to Cortés himself, on 27 February 1525, he learned from a citizen of Tenochtitlan, Mexicalcingo, that Cuauhtémoc, Coanacoch (the ruler of Texcoco), and Tetlepanquetzal, the ruler of Tlacopan, were plotting his death. Cortés interrogated them until each confessed and then had Cuauhtémoc, Tetlepanquetzal, and another lord, Tlacatlec, hanged. Cortés wrote that the other lords would be too frightened to plot against him again, as they believed he had uncovered the plan through magic powers. Cortés's account is supported by the Historian Francisco López de Gómara.

The modern-day town of Ixcateopan in the state of Guerrero is home to an ossuary purportedly containing Cuauhtémoc's remains. Archeologist Eulalia Guzmán, a "passionate indigenista", excavated the bones in 1949, which were discovered shortly after bones of Cortés, found in Mexico City, had been authenticated by the Instituto Nacional de Antropología e Historia (INAH). Initially, Mexican scholars congratulated Guzmán, but after a similar examination by scholars at INAH, their authenticity as Cuauhtemoc's was rejected, as the bones in the ossuary belonged to several different persons, several of them seemingly women. The finding caused a public uproar. A panel assembled by Guzmán gave support to the initial contention. The Secretariat of Public Education (SEP) had another panel examine the bones, which gave support to INAH's original finding, but did not report on the finding publicly. A scholarly study of the controversy was published in 2011 and argued that the available data suggests that the grave is an elaborate hoax prepared by a local of Ichcateopan as a way of generating publicity, and that subsequently supported by Mexican nationalists such as Guzman who wished to use the find for political purposes.

In the 1996 Rage Against The Machine single People of the Sun, lyricist Zack De La Rocha rhymes "When the fifth sun sets get back reclaimed, The spirit of Cuauhtémoc alive and untamed".

Fernando de Alva Cortés Ixtlilxóchitl, a mestizo Historian and descendant of Coanacoch, wrote an account of the executions in the 17th century partly based on Texcocan oral tradition. According to Ixtlilxóchitl, the three lords were joking cheerfully with one another because of a rumor that Cortés had decided to return the expedition to Mexico, when Cortés asked a spy to tell him what they were talking about. The spy reported honestly, but Cortés invented the plot himself. Cuauhtémoc, Coanacoch, and Tetlepanquetzal were hanged as well as eight others. However, Cortés cut down Coanacoch, the last to be hanged, after his brother began rallying his warriors. Coanacoch did not have long to enjoy his reprieve, as Ixtlilxóchitl wrote that he died a few days later.