Sheikh Khalifa has been the president of the United Arab Emirates since 2004, but his role has been largely ceremonial since he suffered a stroke in 2014.
Mohamed bin Zayed al-Nahyan, his half-brother, is now in charge of state affairs.
The al-Nahyan family is thought to be worth $150 billion (£123 billion).
Sheikh Khalifa was not only the president of the UAE, but also the ruler of Abu Dhabi, the oil-rich capital of the UAE’s seven emirates.
The official WAM news agency broke the news of his death.
The presidential affairs ministry declared 40 days of mourning, with flags flying at half-mast beginning Friday and work suspended in the public and private sectors for the first three days.
Sheikh Khalifa became the UAE’s second president in November 2004, succeeding his father as Abu Dhabi’s 16th ruler.
During his first decade in power, he presided over a major restructuring of both the federal and Abu Dhabi governments.
However, following his stroke, he was rarely seen in public, despite continuing to issue rulings.
Sheikh Khalifa was described as a “true partner and friend of the United States” by US President Joe Biden.
“We will continue to strengthen the longstanding ties between the governments and peoples of the United States and the United Arab Emirates in his memory,” Mr Biden said.
The vice-president, Sheikh Mohammed bin Rashid al-Maktoum, ruler of Dubai, will serve as interim president under the UAE constitution.
To elect a new president, the federal council, which includes the rulers of the seven emirates, must meet within 30 days.
- Nepal may relocate Everest Base Camp
- Science points to Robert Pattinson to be declared as the World’s Most Handsome Man 2022
- Amber Heard has the world’s most beautiful face – according to face mapping science
- The Internet will be haunted by the ghost of Internet Explorer for years to come
- Elon Musk: Transgender Daughter applies to legally change her name. She wants nothing to do with father