Bambino Gesu, one of Europe's biggest pediatric hospitals and research centers, is only a short distance away from the Vatican.
The helipad will make the emergency transport of patients, organs and other supplies easier, and will be available 24 hours a day.
Mariella Enoc, the president of Bambino Gesu, said the Holy See's move "will significantly shorten transport times, contributing in many cases to save the lives of children."
She also said Pope Francis was "overjoyed" Bambino Gesu could now use the helipad.
The Holy See owns Bambino Gesu, which provides healthcare for children under Italy's National Healthcare System (NHS), a form of taxpayer-funded care.
The world's first artificial heart transplant occurred in the hospital with a 15-year-old patient in 2010.
