A ministry official told state television on Sunday that the highly contagious variant was detected in a middle-aged Iranian man who had recently travelled back from neighbouring UAE.
The news comes as Iran has, for weeks, experienced relative calm with low infection, hospitalisations and death figures resulting from high vaccination campaign.
More than 60 percent of the eligible population has received two doses of a vaccine, and most people can now receive a booster shot.
The country remain the most affected in the Middle East with more than 6.1 million cases, including over 131,000 deaths.
However, the daily death toll has now dropped to double digits from a high of 709 fatalities registered in late August.
The ministry, on Sunday, announced 50 deaths and 1,968 new cases on Sunday.
Following the discovery of the new variant, health officials in the country have warned of severe consequences for Iran if health protocols are not observed.
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