Sufaira was among six students selected for a youth exchange and service scholarship programme in the US after completing a series of competitive tests.
She was supposed to leave for the US in the first week of August.
"My uncle was a militant, I am not, I had not even been born then. I am shocked at being denied a passport for no fault of my own," said the 17-year-old.
"Those who were selected with me have left for the US. After working so hard for the exams I could not go. It is a shame," she added.
Chief Minister Omar Abdullah on Monday said that Sufaira's passport will be cleared as he has taken up the matter with CID officials.
"Needless to say she will not be denied a passport because of her uncle's past. All such pending cases of previous denials are being cleared," Omar wrote on a social media site. "I have asked the CID to look into the passport case of Sufaira. Will revert with the facts once I have them," he added.
The chairperson of the orphanage where Sufaira is studying said that when he went to confirm from the CID officials about her passport, they denied, saying that they have received 'adverse remarks'. "The CID official told me that they have got adverse remarks about her as her uncle was a militant," said the chairperson of Banaat hostel, Zahoor Ahmed Tak.
This is not the first time that a Kashmiri youth has been denied a passport because of a relative who has militant links. Last week, an engineer, Mehraj-ul-Asrar, was denied a passport because of his father's former links with the Jammu Kashmir Liberation Front (JKLF). However, soon after the intervention of the media, the government said that it had cleared the youth's passport.