Nefertem was born before the world existed, in the dark waters of Nun, the infinite ocean of chaos from which all creation would eventually emerge. In the cosmology of Heliopolis, the city of the sun, the creator god Atum arose from these waters and brought forth the first dry land, the first light, and the first gods. But before Atum could act, a single blue water-lily, Nymphaea caerulea, floated on the surface of Nun, its bud sealed tight against the darkness. As the first rays of dawn touched the water, the bud opened, and from its golden heart rose Nefertem, the Beautiful Atum, the perfect youthful form of the creator in the moment of his first awakening. His name itself declared his nature: nefer meant "beautiful" or "perfect," and tem was an abbreviation of Atum, making him the "Perfect Atum" or "Beautiful One who Completes."

In the Pyramid Texts of the Old Kingdom, the oldest religious writings in the world, Nefertem appears as "the lotus blossom which is before the nose of Re," the sun god whose barque crossed the heavens each day. The image was both literal and cosmic: each morning, as the sun rose from the eastern horizon, it was Nefertem who greeted him, offering the fresh scent of the blue lotus to revive the aging creator. The Egyptians observed that the blue water-lily closed its petals at night and opened them at dawn, a daily resurrection that mirrored the sun's own journey through the underworld, and they understood Nefertem as the force that made this rebirth possible. Without his perfume, Ra would grow too weary to rise. Without his lotus, the dawn would never break.

The myth of Nefertem's tears is one of the most poignant creation stories in Egyptian religion. According to one version of the Heliopolitan cosmogony, Nefertem wept because he was alone in the vast emptiness of Nun, the first conscious being in a universe without companions. His tears fell into the waters and became the first human beings, fashioned from the divine sorrow of a god who longed for company. It was thought that he was born with every sunrise, matured into Atum during the day, and passed into the world of the dead every sunset, a cycle of birth and death that represented the eternal struggle between maat, the cosmic order, and isfet, the chaos that threatened it. When Atum was later absorbed into Re, becoming Atum-Re, Nefertem emerged as a separate deity, still the child of the morning but now with his own distinct identity and cult.

As the power of Memphis grew, the local creator god Ptah was elevated to supremacy, and Nefertem was drawn into the Memphite theology as the son of Ptah and his consort. The identity of his mother varied: sometimes she was Sekhmet, the lioness goddess of war and plague whose breath could destroy mankind, and sometimes she was Bast, the gentler cat goddess of the home and the hearth. Together they formed the Memphite Triad, the divine family that represented the creative, destructive, and renewing powers of the cosmos. In this role, Nefertem was no longer the creator himself but the son of the creator, the one who beautified and healed what his father had made. He became the patron of perfumers and cosmeticians, the god whose oils and unguents transformed the raw materials of the earth into the scented substances that pleased the gods and protected the living.

The blue water-lily was his sacred plant, and its properties were as practical as they were mystical. The Egyptians used the flower to make perfumes, medicines, and possibly psychoactive concoctions, for the blue lotus contains compounds that induce mild euphoria and relaxation. Nefertem was associated with these effects, and his worship blended the spiritual with the therapeutic. Temple hymns praised him as "He Who Beautifies the Gods," the divine perfumer whose essence lingered on altars and in amulets, and tomb inscriptions promised the deceased that they would "Rise like Nefertem from the blue water lily, to the nostrils of Ra, and come forth upon the horizon each day." The lotus was placed beside mummies in tombs, and its image was carved on coffins, a promise that the dead would experience the same daily resurrection as the sun.

In art, Nefertem was usually depicted as a beautiful young man with a lotus flower on his head, sometimes standing on the back of a lion, sometimes holding a was-sceptre of power. He could also appear with the head of a lion or as a reclining lion or cat, reflecting his connection to Sekhmet and Bast, and occasionally his body was shown wrapped like a mummy with his face and arms unbound, a form that linked him to the resurrection of Osiris, the green-skinned god of the dead who was murdered by his brother Set and resurrected by his wife Isis. The most famous representation of Nefertem in Egyptian art is the wooden bust found in the tomb of Tutankhamun, showing the boy king with his face emerging from a large blue lotus, the petals framing his features like a halo of rebirth. The object is both a portrait and a theological statement: Tutankhamun is Nefertem, the dead king who will rise again with the dawn.

The cult of Nefertem was not centred in a single great temple like that of Amun at Karnak or Ptah at Memphis. Instead, he was worshipped in chapels, workshops, and homes across Egypt. Small bronze and faience statuettes of the god, often no taller than a human hand, were mass-produced and carried as amulets, placed in tombs, or set up in household shrines. The ancient Egyptians believed these tiny images brought good fortune, healing, and protection, and archaeologists have recovered thousands of them from sites across the Nile valley. Nefertem also appears in the temple of Seti I at Abydos, where a chapel was dedicated to him alongside Sokar, the falcon-headed god of the Memphis necropolis, and in the Colonnade Hall of Luxor Temple, where his image was carved among the divine procession. But his most enduring presence was not in stone but in scent: every jar of perfumed oil, every cake of cosmetic, every balm applied to the skin of the living or the wrappings of the dead was an offering to the lotus god.