The infected individual, who is asymptomatic, arrived in the territory from France on 16 November.
The person tested positive while in quarantine and has now been transferred to the hospital's isolation ward.
People arriving in Wallis and Futuna undergo two Covid-19 tests before leaving quarantine.
The first test is done seven days after they arrive and the second is done the day before they leave quarantine.
The latest case was diagnosed after the first such test.