Kimura died today at 2.08 am (local time) in a hospital in Kyotango, Kyoto Prefecture, the local government said in a statement.
After being hospitalised with pneumonia on May 11, Kimura recovered temporarily. However, his condition began to worsen again a few days ago.
Born in Kyoto Prefecture on April 19, 1897, Kimura was recognised as the world's oldest-living man by Guinness World Records in April 2011.
He became the oldest living person in December 2012. Kimura became the longest living man on record on December 28 the same year when he was 115 years and 253 days old, The Japan Times reported.
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He retired in 1962 at the age of 65 after working 45 years in the Japanese post office.
Kimura had seven children, two of whom have already died, 14 grandchildren, 25 great-grandchildren and 15 great-great-grandchildren.
He lived with his eldest son's widow, 83, and his grandson's widow, 59, and attributed his long life to eating small portions of food, and would spend most of his time "in bed".
With the death of Kimura, the oldest living person in the world is now believed to be 115-year-old Misao Okawa, a resident of the city of Osaka.