The boat on which she was travelling carried 45 passengers who had departed from Sfax, Tunisia, rescuers said.
The young girl, who is around 11 and is believed to hail from Sierra Leone, said the vessel sank in a storm.
She was rescued at sea by the sailboat operated by six crew members for the NGO Compass Collective, who were in the area for another operation, at 3:20 a.m. on Wednesday.
Rescuers said the young girl was wearing a life vest and was holding on to a life buoy.
She reached Lampedusa at 6 a.m.
Overall, 356 migrants landed on the Sicilian island overnight before the arrival of the young girl rescued by the Trotamar III.
They were travelling on five boats, including one which was carrying 111 passengers, that were rescued by port authorities, finance police and Frontex officials.
The first boat transported 111 people who hailed from Egypt, Eritrea, Pakistan, Syria, Sudan and Somalia, including 13 women and 11 minors.
The others carried a minimum of 45 and a maximum of 87 passengers from Bangladesh, Syria, Morocco, Sudan and Iran.
All passengers said they had departed from Libya.
Some 618 people have died and 918 gone missing in the central Mediterranean so far this year, the International Organisation for Migration (IOM) said Wednesday.
The central Mediterranean is one of the most widely used channels for illegal migration to Italy and Europe.
The numbers refer to the period from January 1 to December 7, the IOM office in Libya said in its latest update published on X.
In the same period, the UN agency specifies, migrants intercepted at sea and returned to Libya were 20,894.
Of those returned, 18,180 were men, 1500 women, 688 minors and 526 people for whom gender data is not available.
ANSA