The strain, which was first announced by South Africa but has since been discovered to have been present earlier in Europe, has prompted governments around the globe to reimpose travel restrictions, despite warnings from the World Health Organization (WHO) this could do more harm than good.
"One case of the Omicron variant has been detected in the kingdom -- it was a citizen coming from a North African country," a health ministry official told the state SPA news agency on Wednesday.
"He has been put in isolation, as have his contacts, and the necessary health measures have been taken."
Saudi Arabia last week halted flights from seven southern African countries, mirroring similar moves by other government, but travel links with North Africa have remained unaffected.
The kingdom had been lifting some of the remaining restrictions it imposed early in the pandemic, allowing worshipers at the Muslim holy places to resume praying shoulder to shoulder from October.
Since the pandemic started, Saudi Arabia has recorded 549,000 cases of COVID-19, 8,836 of them fatal.
More than 47 million doses of COVID vaccine have been administered in the kingdom, which has a population of nearly 35 million.