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Begum, 20, who left the UK as a schoolgirl to join the Islamic State terror group, has had a ruling by the Special Immigration Appeals Commission from earlier in the year partially overturned by senior judges at the Court of Appeal.
Begum took legal action against the Home Office and argued that she had been unlawfully rendered stateless and left at risk of death or inhuman and degrading treatment.
The Home Office has said that it will challenge the decision, meaning that Begum will not be able to return to the country whilst those proceedings are ongoing.
Lord Justice Flaux, who sat with two other judges, said: "Notwithstanding the national security concerns about Ms Begum, I have reached the firm conclusion that given that the only way in which she can have a fair and effective appeal is to be permitted to come into the United Kingdom to pursue her appeal, fairness and justice must, on the facts of this case, outweigh the national security concerns."
Ms Begum's solicitor Daniel Furner said: "Ms Begum has never had a fair opportunity to give her side of the story. She is not afraid of facing British justice, she welcomes it. But the stripping of her citizenship without a chance to clear her name is not justice, it is the opposite."
Ms Begum's argument focuses on the premise the citizenship of a particular country can only be revoked if the person is entitled to citizenship in another country.
She contested that this decision made her stateless, and that she was unable to effectively challenge the decision against her because she could not return to the UK.
She remains at a refugee camp in Northern Syria.
At a tribunal in February, the initial decision ruled that the removal of her citizenship was lawful because she was 'a citizen of Bangladesh by descent' at the time.
She is thought to have a claim to Bangladeshi citizenship through her mother.
This partial overturning of that decision means the UK government must now find a way to get Ms Begum into the country so she can appear in court in London, despite repeatedly claiming that they would play no part in removing her from Syria.
A Home Office spokesperson said: "This is a very disappointing decision by the Court. We will now apply for permission to appeal this judgement, and to stay its effects pending any onward appeal.
"The government's top priority remains maintaining our national security and keeping the public safe."
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