The discovery worsened the prospects of the virus having already spread further in the capital of Italy, since most Vatican employees live in Rome and those who live in the Vatican frequently enter and leave the city state.
The death toll in Italy, the worst-hit European country, stood at 148 on Thursday. The north of the country has been the most heavily hit.
Vatican spokesman Matteo Bruni said the case was diagnosed on Thursday and that services in Vatican clinics had been suspended to sanitize the areas.
Most Vatican employees who use its health services live in Italy on the other side of the border with the 108-acre city state.
Bruni gave no details on whether the person who tested positive was such an employee or among the relatively few clergy or guards who live inside its walls.
Italian health authorities said that, as of Thursday, 42 people had tested positive for coronavirus in Rome province.
Pope Francis cancelled a Lent retreat for the first time in his papacy, but the Vatican has said he is suffering only from a cold that is “without symptoms related to other pathologies.”
The Vatican has also said it is studying measures to modify the pope’s activities to avoid the spread of coronavirus in coordination with measures by the Italian government, which include encouraging people not to gather in large numbers.
Tens of thousands of people flock to St. Peter’s Square every Sunday to listen to the pope give his weekly blessing and message from a window of the Vatican Apostolic Palace overlooking the square.
Thousands of others attend his weekly general audience, which is held either outdoors in the square or in a large audience hall inside the Vatican, depending on the weather.