According to a letter sent to her mother, Home Secretary Sajid Javid ordered the move against the 19-year-old Londoner who wants to return to the UK with her newly born child as the so-called caliphate crumbles.
She was part of a trio of girls from Bethnal Green Academy to travel to the war-torn nation to support the terror group in February 2015.
Her family's lawyer, Tasnime Akunjee, described them as "very disappointed" over the move and said they are "considering all legal avenues to challenge this decision".
ITV News reported a letter from the Home Office that was received by Ms Begum's mother on Tuesday.
"Please find enclosed papers that relate to a decision taken by the Home Secretary, to deprive your daughter, Shamima Begum, of her British citizenship," it read.
"In light of the circumstances of your daughter, the notice of the Home Secretary's decision has been served of file today (19 February), and the order removing her British citizenship has subsequently been made."
The letter asked the mother to inform her daughter of the decision, as well as her right to appeal.
The move comes after she returned to the public eye when she was found heavily pregnant living in a refugee camp in northern Syria.
She gave birth to a boy over the weekend, having already lost two children, and made pleas for forgiveness and to be accepted back in the UK.
Metropolitan Police Commissioner Cressida Dick has signalled she could be arrested and investigated if she returns to Britain.
When she left the UK, the then chief of counter-terror policing Sir Mark Rowley suggested that she might be treated as a victim of grooming.
International law forbids nations from making people stateless by revoking their only citizenship, but it is possible Ms Begum, who is of Bangladeshi heritage, held dual citizenship.
Government guidance from 2017 states that the Home Secretary has the power to order the deprivation if it would be "conducive to the public good", as long as they are not left without any citizenship.
A Home Office spokesman said he could not discuss individual cases, but added: "We don't leave people stateless."