A Division bench of the high court also issued a notice of motion to the Haryana government and the CBI on his family's plea seeking a probe by the central agency into the matter.
"The high court today stayed the trial proceedings of the court in Faridabad," said Arshdeep Singh Cheema, the counsel for Mr Khan's father Jalaluddin.
The plea for a CBI probe into the killing of Junaid Khan came up for hearing before the division bench comprising Justices Mahesh Grover and Raj Shekhar Attri.
Mr Khan's father had last week challenged the November 27 judgement of a single bench that dismissed the petition seeking a CBI probe into the alleged lynching by filing an appeal.
The high court single bench had said, "during the course of the hearing, the complainant has not been able to show that there are serious flaws in the investigation, which would lead to the conclusion that the same is shoddy or tainted.
"Besides, there is nothing to show that the incident has any national or international ramifications. It is, thus, not a fit case to exercise extraordinary power to hand over the investigation to the CBI," the high court single bench had said.
While seeking a probe by the CBI, the appeal filed through advocate Cheema mentions "the true nature of the crime has been subjected to a cover up. The conduct of the named accused and others as a lynching mob has been concealed. It has been projected as if the occurrence were sudden without any element of perpetrators having acted as in conspiracy or an unlawful assembly".
The case will now come up for hearing on January 11, Cheema said.
Jalaluddin, through his counsel, had earlier filed the petition on October 26, seeking a probe by an independent agency, such as the Central Bureau of Investigation, in the lynching case.
The petitioner also had demanded a stay on the trial in a Faridabad court.
Mr Khan, who had boarded a Mathura-bound train from Delhi, was allegedly stabbed to death when he, along with his brothers and cousins, was returning home to Khandawali village after shopping for Eid in Delhi in June.
His body was dumped near Asaoti village in Faridabad district.