In his first act as emperor, he will inherit Japan's Imperial Treasures in a deeply symbolic ceremony.
The emperor in Japan holds no political power but serves as a national symbol.
Emperor Akihito, 85, who chose to abdicate due to his age and failing health, stepped down on Tuesday.
"I hereby pray for the well-being and happiness of our country and people of the world," he said in his final address.
The new imperial era "Reiwa", whose name signifies order and harmony, began at midnight local time, and will last as long as Naruhito's reign.
What will happen at the ceremony?
The Kenji-to-Shokei-no-gi - or Ceremony for Inheriting the Imperial Regalia and Seals - will begin at 10:15 local time (01:15 GMT).
Naruhito, 59, will receive three objects - a mirror, sword and gem - which are passed down through generations of emperors and are seen as the symbols of imperial power.
He will then give his first address as new emperor.