The court has provided protection for a man tricked into visiting the country by his parents.
Shivy, 18, is technically an Indian citizen – but has been living in the USA for fifteen years.
The court move comes after he alleged that his parents tried to forcibly marry him off to a man after tricking him into the trip.
Shivy – who prefers to be referred to by his first name only – also says they seized his passport and green card.
His parents have refused to comment on the allegations.
He told BBC Hindi that his parents told him that they had brought him to the north Indian city of Agra to “fix” him – after they found out that he had a girlfriend back in the US.
“They took away my mobile phone and laptop even while we were in America, but I still never imagined then that our annual holiday to India in July would have any other motive,” he said.
The Delhi High Court deemed the allegations as nothing short of “bigotry”, before claiming that India was “a land of tolerance”.
Transgender activists and the support group Nazariya arranged legal counsel and shelter for Shivy in Delhi after he ran away from Agra earlier this month.
The University of California claims that he fears for their safety – as well as his own – after his father and some men posing as police officers came to the activist’s home.
He has asked the High Court to help him retrieve both his passport and green card so that he can return to the United States.
The Delhi High Court has asked his parents and state police to respond to the allegations immediately.
Indian’s parliament has been urged to include intersex people in a bill to protect the rights of trans people.
The Transgender Rights Bill 2014 was passed in the upper house of India’s parliament.
However activists are now urging for the bill to include intersex rights, before it is signed into law.