City of Glasgow College student Majid Ali was recently held at Dungavel Detention Centre in Lanarkshire.
Supporters believe he was deported on Tuesday night. The Home Office said it did not comment on individual cases.
Mr Ali had accused the Pakistani authorities of killing his uncle and cousin and abducting his brother.
He first claimed asylum in the UK in 2011 after stating that his brother was the victim of an enforced "disappearance" by Pakistani authorities.
More recently, Mr Ali claimed that his family home in the Balochistan province was raided by government forces, and his uncle and cousin were shot and killed.
The volatile province, in the south west of Pakistan, has seen conflict between government forces and groups from the region who want more political autonomy or independence and a greater share of revenue from natural resources.
The National Union of Students (NUS) had been running a campaign to keep Mr Ali in the UK.
Earlier this week, NUS Scotland president Gordon Maloney said: "We are deeply concerned for Majid's safety if he is forced home.
"We all recognise that nobody deserves the kind of treatment he has received in this country, or the grave danger that might await him on his forced return home."
The campaign had been supported by SNP MP for Glasgow South West, Chris Stephens, who wrote to the immigration minister and Scottish secretary and attempted to raise the case in the House of Commons.
Mr Stephens had said it was "fairly obvious to anyone looking at this case that Majid should be allowed to stay as there would be a genuine fear for his life if he was deported".
A Scottish-based student is thought to have been deported to Pakistan despite claims he faces political persecution and possible death in his homeland.