The execution brings to 12 the total number of death sentences carried out since Prime Minister Shinzo Abe took power in 2012.
Tsukasa Kanda, 44, was hanged for killing 31-year-old Rie Isogai in Nagoya, central Japan, in 2007.
He met his two accomplices via a mobile phone-based web service and the three of them together devised a plan to target a random woman victim.
The men kidnapped Isogai from a Nagoya street and suffocated her by wrapping her head and neck with a plastic bag, adhesive tape and rope, before battering her head with a hammer, according to Justice Ministry records.
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"After a series of careful reviews, I ordered the execution," she said.
Kanda's accomplices are serving life sentences.
Kanda did not appeal his death sentence after the original district court ruling.
Japan and the United States are the only major advanced industrial nations that continue to have capital punishment.
Surveys have shown the death penalty has overwhelming public support, despite repeated protests from European governments and human rights groups.