“The government of the Republic of Burundi announces with great sadness the unexpected death of His Excellency Pierre Nkurunziza … following heart failure,” said a message on social media.
It said there would be seven days of national mourning.
Nkurunziza swept to power in 2005 when he was selected by parliament.
The country descended into political crisis and violence after he sought a third presidential term from 2015.
At least 1,200 people died and hundreds of thousands of were displaced as authorities cracked down on opposition parties as well as the media.
Burundi’s President Pierre Nkurunziza, aged 55, has died after suffering a cardiac arrest, the government says.
He was admitted to hospital on Saturday after feeling unwell, his condition improved but on Monday he had a cardiac arrest and efforts to revive him were unsuccessful, officials say.
After 15 years in power, Mr Nkurunziza was due to step down in August.
Late last month, Burundi’s First Lady Denise Nkurunziza was admitted at the Aga Khan University Hospital, Nairobi, after she reportedly contracted the novel coronavirus.