The hanging of Tokuhisa Kumagai was the sixth such this year since the government of Prime Minister Shinzo Abe came to power, Kyodo News reported.
Kumagai was convicted in the shooting death of 77-year-old Fumio Shimizu and taking his money bag. He was also convicted of shooting and seriously injuring a Tokyo subway station worker in a failed robbery in the same year.
In April, two men were executed for killing two other men. That followed the hangings of three men in February, Kyodo said.
Last year, seven people were executed under the former administration of the Democratic Party of Japan. Currently there are about 130 inmates on the death row.
Japan is one of a few developed countries to have the death penalty. Kyodo said. The Justice ministry does not notify inmates of the date their execution in advance.