She was reportedly infected with the more infectious N501Y mutated strain, and is being treated in Tuen Mun Hospital.
The teenager has a high viral load, the source said, and had a fever, sore throat and experienced a loss of taste.
Authorities are said to be investigating where the girl, who lives in Tin Shui Wai and has no travel history, might have caught the virus.
Hong Kong has gone 42 days without an untraceable Covid case, with all confirmed cases over the past two weeks being imported infections.
The total includes an imported case confirmed by health officials on Friday, involving a 21-year-old woman who flew in from Austria.
She had been undergoing quarantine at the Ramada Hong Kong Harbour View hotel in Sai Ying Pun when she tested positive for the virus.
Since the start of the pandemic, the city has recorded 11,850 confirmed cases with 210 related deaths.
Last updated: 2021-06-04 HKT 16:15