Justice A S Dave ordered the medical officer at the Surendranagar civil hospital to verify if she is physically and mentally fit to undergo the abortion.
The court has asked the doctor to submit the report by May 4. The girl has also been told to be present in the court on that day.
The girl's parents move the Gujarat High Court after their appeal was turned down by a local court.
The teenager, who belong to poor family in Dhrangadhra of Surendranagar district, was working as a domestic help at Ghanshyamsinh Rajput's house.
She conceived after she was repeatedly raped by her employer.
Her parents came to know about the incident only when she was two-months pregnant. They met a doctor for their daughter's abortion, who in turn asked them to seek permission from the court.