According to Ignatios the Deacon, the author of the Short History was the son of pious parents, Theodore and Eudokia, and he was a born Constantinopolitan. Patriarch Photios, who wrote in the second half of the ninth century, claimed that Nikephoros was related to the Patriarch Tarasios. In one of his letters to Pope Nicholas I, Photios wrote:

Further, for Patriarch Photios, who himself had to defend his patriarchal ordination before the pope, Tarasios and Nikephoros were not only his kin, as he pointed out in the letter to Nicholas I, but also ‘firm guardians of the rules, defenders of piety, torchbearers when the word of godly science and life was attacked in this world’ (οὗτοι γὰρ τῶν ϰανόνων ἀϰριβϵῖς φύƛαϰϵς, τῆς ϵὐσϵβϵίας ὑπέρμαχοι, τῆς δυσσϵβϵίας ϰατήγοροι, φωστῆρϵς ἐν ϰόσμῳ ϰατὰ τὸ θϵῖον ƛόγιον ƛόγον ζωῆς ἐπέχοντϵς). Photios further emphasized that Nikephoros was not only Tarasios's worthy successor on the patriarchal throne but also his relative, and thus Photios's relative as well.

The exact year of Nikephoros's birth cannot be precisely determined according to his Life by Ignatios, although it can be supposed that he was born sometime during the reign of the Emperor Constantine V (741-775). Nikephoros's father Theodore obviously belonged to court aristocratic circles, since at one time he served as a secretary at the court of Constantine V.5 However, the Iconoclasm of the emperor did not prevent Theodore from firmly confessing his strong adherence to icons in the presence of the emperor himself.