The accused, aged 30 years, was arrested from Dhule in Maharashtra on Saturday. He was produced in a court in Faridabad on Sunday and police remand was sought.
The identity of the man is not being revealed by the police quoting legal provisions. He belongs to Palwal district in Haryana and was working as a security guard in a private company in Delhi, Government Railway Police (GRP) Deputy Commissioner of Police (DCP) Kamal Dev told media in Faridabad on Sunday.
"We are interrogating him. It is an ongoing, open investigation. A final picture will emerge only after completion of the interrogation," he said.
"The accused was identified after a thorough, continuous effort over the last 15 days by our teams," Dev said.
He added that the accused stayed at his home (in Palwal district) and went to Dhule later to someone known to him. He started working there.
The DCP said that the murder weapon, a knife, was yet to be recovered. He said the accused had admitted to the crime.
"There is no reference to beef in the complaint of the victims and also questioning of the accused," Dev said in reply to a question whether the killing was linked to objections over beef.
Meanwhile, the parents of Junaid have demanded the death penalty for the accused.
Junaid Khan was brutally beaten and stabbed to death on a local train at Ballabhgarh in Haryana on June 22 by a group of people following an argument over seats.
The murder triggered nationwide outrage.
Junaid and cousin brothers Hasim Moin and Shakir Moin had boarded the EMU train going from Ghaziabad to Mathura after Eid shopping on June 22. The accused, along with around a dozen other persons, boarded the train at Okhla and ordered Junaid and his brothers to give them their seats.
When they refused, they brutally beat the three and also stabbed them and dumped them at Asaoti railway station in Palwal district.
The police have made five arrests earlier in this case.
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