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".

6 February 2017 Last updated at 17:15 GMT
This year features many famous faces and locations from around the world.
You may recognise Pikotaro, who became an internet legend with his song Pen-Pineapple-Apple-Pen.
Even the President of the United States, Donald Trump, makes an appearance.
The biggest sculpture is a frosty version of the Arc de Triomphe - a famous monument in Paris. They even raised a French flag in front of it in a special ceremony.
Check out the video to see some super snow sculpting skills

The Storr, a geological feature of the landscape in Trotternish, Skye, was used for creating scenes in the new movie directed by Steven Spielberg.
Tourism body VisitBritain has promoted The Storr in its new campaign called Oh My Giant Britain (OMGB).
It also features the film's locations in England.
Images of actress Ruby Barnhill, who plays lead character Sophie in the film, at The Storr, Big Ben in London and the Angel of the North near Gateshead have been released on social media.
The BFG launches in the US on 1 July and in the UK on 22 July.
Skye is a favourite with film-makers and provided backdrops for Stardust, which starred Michelle Pfieffer, big budget sci-fi Prometheus and also Snow White and the Huntsman, Keanu Reeves' film 47 Ronin and the latest film adaption of Macbeth.
Last month it emerged that the production team behind The BFG were helped by Highland's Council's small tourism and film unit with its inquiries about locations on Skye.

The average rent stands at Â£774 in England and Wales, according to data from Your Move and Reeds Rains.
It said that rental costs had risen by 0.8% in April compared with March.
Adrian Gill, LSL director, said: "Momentum is fuelled by a fundamental shortage of housing and given oxygen by renewed wage growth."
The latest official figures from the Office for National Statistics (ONS) suggested that the cost of renting a home from a private landlord in Britain rose by 2.1% in the year to the end of March.
Campbell Robb, chief executive of housing charity Shelter, said: "Our housing shortage has been decades in the making, and only bold and immediate action can fix it.
"No matter how hard they work or save, an entire generation is being forced to watch their dreams of a stable future slip through their fingers, stuck in properties where rents eat up their salaries and short term contracts leave them with no stability at all."
A Scottish-based student is thought to have been deported to Pakistan despite claims he faces political persecution and possible death in his homeland.
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The Sapporo Snow Festival has started in Japan, featuring its famous collection of snow sculptures!
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Visits to the Isle of Skye could be boosted by a tourism campaign based on the film adaption of Roald Dahl's story The Big Friendly Giant.
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The cost of renting a home rose by 4.6% in the year to the end of April, the fastest rise since November 2010, property group LSL has said.