But, after a series of traditional rituals inside the imperial palace in Tokyo, his ascension has now been formalised.
The ceremony comes as Japan reels from the effects of Typhoon Hagibis, which left almost 80 people dead.
A celebration parade was postponed out of respect for the victims and their families.
What happened at the ceremony?
The Sokui no Rei - or the Ceremony of Accession - saw Emperor Naruhito inside the 6.5m-high Takamikura throne.
He read out a formal proclamation, dressed in a yellow-orange robe worn only by emperors on special occasions.
"I swear that I will act according to the constitution and fulfil my responsibility as the symbol of the state and of the unity of the people," he said, according to a Reuters translation.
His wife Empress Masako, reportedly clothed in 12 layers of robes, was seen in a separate smaller throne.
Prime Minister Shinzo Abe delivered a congratulatory address, followed by shouts of "Banzai!" - translated as "long live the emperor".
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Hundreds of foreign dignitaries, including the UK's Prince Charles, were in attendance.
The emperor will later host a tea party for foreign royalty, while Mr Abe will host a banquet in the evening.
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Small crowds turned out on Tuesday morning outside the palace despite a heavy downpour.
"Today is an important day for the new emperor and the empress," 78-year-old Shuichi Hachinuma, who had travelled to Tokyo, told news agency AFP.
"I feel the emperor is closer to us, compared to in the past... I want him to send a message of peace."
The torrential winds and rains cleared just as the ceremony began.
Some social media users claimed a rainbow appeared just in time for the ceremony.