The guards have, however, denied the charges of discrimination and said they only stopped her from entering a men's toilet.
Chief Proctor O.P. Rai has instituted a three-member committee to probe into the allegation.
According to reports, the complainant, who is studying arts and is an active member of BHU's SC/ST Students' Programme Organising Committee, said she was working at the Bahujan Helpdesk near Mahila Mahavidyalaya premises for the past five days to guide college freshmen.
On Thursday, she tried to enter the Mahila Mahavidyalaya premises to use a toilet when the guards stopped her. They allegedly asked her to go to the hospital or college campus for using a toilet.
"Their attitude was discriminatory, inhuman and illegal," the student said in her written complaint to the Chief Proctor. She has demanded 'immediate disciplinary action' against the guards.
On Friday, Rai said he had received the student's complaint and met her personally to hear out her grievances.
"The accused guards were summoned. They have claimed that they stopped her because she was entering a men's toilet. We have, however, formed a panel, which includes two women officials, to probe into the matter," Rai said. He said action would be taken based on the committee's report.
( With inputs from IANS )