In just over two months, Saudi Arabia has beheaded almost half the number of foreigners and Saudis executed during all of 2014, according to AFP tallies.
Joven Esteva was found guilty of stabbing the Saudi in the chest in 2007.
"The perpetrator had worked as a driver for him," an interior ministry statement carried by the official Saudi Press Agency said.
Authorities carried out the sentence against Esteva in Riyadh, adding to what Amnesty International calls an unprecedented pace of executions in the kingdom this year.
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"Regrettably, despite efforts of the Philippine government, (the) family of the victim refused to grant forgiveness," he said, without giving other details.
London-based Amnesty says the number of death sentences carried out so far this year in Saudi Arabia has been almost four times that for the same period in 2014.
The death penalty for murderers aims "to maintain security, serve justice, and implement the provisions of God," the interior ministry says.
Rape, murder, apostasy, armed robbery and drug trafficking are all punishable by death under Saudi Arabia's version of Islamic sharia law.
There have been around 80 executions annually in the kingdom since 2011, with 87 last year by AFP's tally.
Saudi Arabia is among the world's top executioners, according to Amnesty.
The kingdom beheaded another Filipino worker, Carlito Lana, on December 12 for shooting a Saudi man and then running him over with a car.
About 10 per cent of Filipinos work overseas, attracted by the promise of salaries higher than they can earn at home. Their remittances are a vital support for the Philippines economy.
Manila is seeking to have the impending execution by firing squad stopped by lodging an appeal to have her case reviewed by the judiciary there.