This means she is now effectively banned from entering the UK.
The move came after the teenager from Bethnal Green was thrust back into the public eye when she was found heavily pregnant in a refugee camp in northern Syria.
She says she has already lost two children to illness in the war-torn country and wants to return to the UK with her son whom she gave birth to at the weekend.
Ms Begum’s lawyer Tasnime Akunjee told The Independent her family planned to launch a legal challenge against the home secretary’s decision.
Mr Akunjee said Ms Begum, who is of Bangladeshi heritage, was born in the UK, has “never had a Bangladeshi passport”, and does not have dual citizenship.
“Our position is that to all practical purposes she has been made stateless,” he said.
The lawyer also accused the government of making Ms Begum’s days-old son stateless, and leaving them both “stuck” in a Syrian detention camp.
He added: “This is a delaying tactic. The government is not going to win this, there is case law saying people in these circumstances are stateless and we will win but how long will that take.”
The Home Office declined to comment on Mr Akunjee’s allegations on Tuesday but said: “We do not make people stateless.”
In a letter addressed to Ms Begum’s mother, the Home Office asked her to inform her daughter of its decision, as well as her right to appeal.
Lord Carlile, former independent reviewer of terrorism legislation, said Ms Begum could challenge the decision, but that she could be stuck in Syria for at least two years during the process.
“It could run for a very long time through the courts,” he told BBC Breakfast. “I suspect that the result is going to be that she will stay where she is for maybe two years at least.”
Ms Begum’s family is of Bangladeshi descent and she married a Dutch foreign fighter but the citizenship of their child is unclear.
In a previous case a baby born to a female Isis supporter in Syria was only given British citizenship after a DNA test proved her parentage. The nationality of the baby's father in that case has not been made public.
Government guidance states that the home secretary can deprive citizenship for the “public good” if a person can apply for alternative nationality.
Register for free to continue reading
Registration is a free and easy way to support our truly independent journalism
By registering, you will also enjoy limited access to Premium articles, exclusive newsletters, commenting, and virtual events with our leading journalists
Already have an account? sign in
Join our new commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies