The year of Temüjin's birth is disputed, as historians favour different dates: 1155, 1162 or 1167. Some traditions place his birth in the Year of the Pig, which was either 1155 or 1167. While a dating to 1155 is supported by the writings of both Zhao Hong and Rashid al-Din, other major sources such as the History of Yuan and the Shengwu favour the year 1162. The 1167 dating, favoured by Paul Pelliot, is derived from a minor source—a text of the Yuan artist Yang Weizhen—but is more compatible with the events of Genghis Khan's life than a 1155 placement, which implies that he did not have children until after the age of thirty and continued actively campaigning into his seventh decade. 1162 remains the most accepted date; the historian Paul Ratchnevsky notes that Temüjin himself may not have known the truth. The location of Temüjin's birth is similarly debated: the Secret History records his birthplace as Delüün Boldog on the Onon River, but this has been placed at either Dadal in Khentii Province or in southern Agin-Buryat Okrug, Russia.

Temüjin was born into the Borjigin clan of the Mongol tribe to Yesügei, a chieftain who claimed descent from the legendary warlord Bodonchar Munkhag, and his principal wife Hö'elün, originally of the Olkhonud clan, whom Yesügei had abducted from her Merkit bridegroom Chiledu. The origin of his birth-name is contested: the earliest traditions hold that his father had just returned from a successful campaign against the Tatars with a captive named Temüchin-uge, after whom he named the newborn in celebration of his victory, while later traditions highlight the root temür (meaning 'iron') and connect to theories that "Temüjin" means 'blacksmith'. Yesügei and Hö'elün had three younger sons after Temüjin: Qasar, Hachiun, and Temüge, as well as one daughter, Temülen. Temüjin also had two half-brothers, Behter and Belgutei, from Yesügei's second wife Sochigel, whose identity is uncertain. The siblings grew up at Yesugei's main camp on the banks of the Onon, where they learned how to ride a horse and shoot a bow.

When Temüjin was eight years old, Yesügei decided to betroth him to a suitable girl. He took his heir to the pastures of Hö'elün's prestigious Onggirat tribe, which had intermarried with the Mongols on many previous occasions. There, he arranged a betrothal between Temüjin and Börte, the daughter of an Onggirat chieftain named Dei Sechen . As the betrothal meant Yesügei would gain a powerful ally, and as Börte commanded a high bride price, Dei Sechen held the stronger negotiating position, and demanded that Temüjin remain in his household to work off his future debt. Accepting this condition, Yesügei requested a meal from a band of Tatars he encountered while riding homewards alone, relying on the steppe tradition of hospitality to strangers. However, the Tatars recognised their old enemy, and slipped poison into his food. Yesügei gradually sickened but managed to return home; close to death, he requested a trusted retainer called Münglig to retrieve Temüjin from the Onggirat. He died soon after.

At age eight, Temüjin was betrothed by his father Yesügei to Börte, daughter of Onggirat chieftain Dei Sechen, to secure an alliance through marriage. This union necessitated Temüjin to stay with the Onggirats, fulfilling obligations towards his future bride's family. On his return journey, Yesügei, poisoned by Tatars he encountered, barely made it home before succumbing to the poison. Before dying, he arranged for Temüjin's retrieval from the Onggirats through a loyal retainer, Münglig.