Masanori Kawasaki, 68, was convicted of stabbing three people to death – including a three-year-old girl – as they slept, after breaking into their house in Kagawa, western Japan, in 2007.
“It was an extremely cruel case,” Justice Minister Sadakazu Tanigaki told reporters.
“I ordered the execution after prudent consideration,” he said.
Apart from the United States, Japan is the only major industrialised democracy to use capital punishment.
Surveys have showed the death penalty has overwhelming public support despite repeated protests from European governments and human rights groups.
Separately, another death-row inmate, 60, died in prison of acute respiratory failure on Thursday, local media reported.
Shigeo Okazaki, a former police officer, was sentenced to death in 2004 after he kidnapped and killed two people in 1986 and 1989, Jiji Press said.
Japan now has 129 inmates on death row, according to local media.
Tokyo did not execute anyone in 2011, the first full year in nearly two decades without an execution amid muted debate on the rights and wrongs of the practice.
But in March 2012 it abruptly resumed its use of capital punishment, dispatching three multiple murderers.
International advocacy groups say Japan’s system is cruel because inmates can wait for their executions for many years in solitary confinement and are only told of their impending death a few hours ahead of time.
There have also been a number of high-profile miscarriages of justice exposed in recent years, including Iwao Hakamada, who was released from jail earlier this year, aged 78, after decades on death row for a multiple murder he did not commit.
Hakamada, who was believed to be the world’s longest-serving death row inmate, was the victim of a flawed investigation in which evidence was fabricated.