"The Royal Court mourns His Royal Highness... who passed away this morning at Mayo Clinic Hospital in the United States of America," the Bahrain News Agency (BNA) said.
The country will hold a week of official mourning.
The burial ceremony will take place upon the repatriation of his body and the funeral will be limited to a specific number of relatives, the statement said.
Prince Khalifa received World Peace Culture Award on 6 August 2017. Under the 2002 Constitution he lost some of his powers, with the King now having the authority to appoint and (along with the Bahraini parliament) dismiss ministers.
HM the King ordered the announcement of an official mourning for a week during which flags will be flown at half-mast
Government ministries and departments will be closed for three days starting Thursday.