In a statement, the UN agency said that the victim was an 83-year-old man from the eastern region of Al-Ahsaa, where an outbreak began in a healthcare facility in April.
The man fell ill on May 27 and died on May 31, WHO said.
"Globally, from September 2012 to date, WHO has been informed of a total of 55 laboratory-confirmed cases of infection with MERS-CoV, including 31 deaths," it said in a statement.
Previously known as novel coronavirus, the disease was last month renamed Middle East Respiratory Syndrome Coronavirus, or MERS-CoV, reflecting the fact that the bulk of the cases are in that region.
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WHO records cases and deaths according to the country where the individual is thought to have caught the disease, rather than where they died, and its Saudi toll includes a person who subsequently died in Britain.
One person has died in France after catching the disease in the United Arab Emirates, just like a fatality in Germany.
There have also been two cases in Jordan, both of them fatal, as well as two in Qatar, with those patients treated in Britain and Germany