The 19-year-old, who recently gave birth to her child at a Syrian refugee camp, has been urging authorities to let her return to the UK.
On Tuesday, the UK Home Office issued a letter to her family in the UK, said a report on ITV, which obtained a copy of the letter.
"Please find enclosed papers that relate to a decision taken by the Home Secretary, to deprive your daughter, Shamima Begum, of her British citizenship," the letter read.
The letter urged the family to make Shamima aware of the decision, and added that she had a right to appeal.
In 2015, she and two school friends from fled the UK via Turkey, where they made their way to Syria and were married off to Islamic State fighters.
She insisted that she was "not a threat". "I don't have any weapons; I don't want to hurt anyone even if I did have weapons.”
In a statement, the Home Office defended the decision made by Home Secretary Sajid Javid. "In order to protect this country, he has the power to deprive someone of their British citizenship where it would not render them stateless.
"Now the Home Secretary can't do that if that would render the person stateless, but he says Shamima Begum has Bangladeshi nationality and therefore he's entitled to take away her British nationality," said a spokesperson.
"We do not comment on individual cases, but any decisions to deprive individuals of their citizenship are based on all available evidence and not taken lightly."
International law forbids nations from making people stateless by revoking their only citizenship.
Shamima earlier told the BBC that she did not have a Bangladeshi passport and had never been to the country.
As for her newborn, he is presumably entitled to British citizenship because he was born to a British parent before the decision was taken.
If Shamima’s mother is a Bangladeshi national then the daughter would also be a citizen, Lord Carlile, a former independent reviewer of terrorism legislation, told the BBC.
"Family are very disappointed with the Home Office's intention to have an order made depriving Shamima of her citizenship,” said Tasnime Akunjee, the family's lawyer, posted on Twitter.
"We are considering all legal avenues to challenge this decision."