Shamima Begum, who now wants to return home after giving birth in a refugee camp in Syria last weekend, said the order was "unjust".
"I am a bit shocked," she told ITV News after learning of the move which was announced in a letter Tuesday from Britain's interior ministry to her mother in London.
"It's a bit upsetting and frustrating. I feel like it's a bit unjust on me and my son."
Begum's fate has stirred controversy since she and two friends fled her east London home to join the terror network four years ago when she was aged just 15.
The case highlights a dilemma facing many European countries, divided over whether to allow jihadists and IS sympathisers home to face prosecution or barring them over security concerns as the so-called "caliphate" crumbles.
A spokeswoman for the interior ministry said on Tuesday it would not comment on individual cases, "but any decisions to deprive individuals of their citizenship are based on all available evidence and not taken lightly".
She added that interior minister Sajid Javid was intent on prioritising "the safety and security of Britain and the people who live here".
"In order to protect this country, he has the power to deprive someone of their British citizenship where it would not render them stateless."
Begum gave birth to her third child at the weekend, and appealed to British authorities to show "compassion" by allowing her to raise the baby in Britain -- while expressing no regret over having joined IS.
'All legal avenues'
In the ministry's letter sent to Begum's mother, it said the teen had the right to appeal the order.
A lawyer for her family said it was disappointed with the move.
"(The) family are very disappointed with the... intention to have an order made depriving Shamima of her citizenship," Tasnime Akunjee said on Twitter.
"We are considering all legal avenues to challenge this decision."
Begum, who is of Bangladeshi heritage, was born in Britain, has never had a Bangladeshi passport and is not a dual citizen, according to Akunjee.
The interior ministry reportedly believes that she is entitled to claim citizenship in the south Asian country.
Chiranjiv Sarker, head of the consular wing and dual nationality issues at Bangladesh's foreign ministry, told AFP it was aware of the case but had not received any contact from the family.
"So far none of her family members (has) approached us," he said. "What I learn from newspapers is that Shamima was trying to return to Britain."
He added that, if approached, the ministry would need to try to verify Begum's Bangladeshi heritage to assess any possible eligibility for citizenship.
Trump call rebuffed
Begum is currently in a refugee camp in northeast Syria where she fled to escape fighting in the east of the country along with hundreds of other people with links to IS.
She said she has previously given birth to two other children after marrying in Syria. Both children have died, apparently from illness and malnutrition.
Begum fled Britain with Kadiza Sultana, who has since been reported killed, and Amira Abase.
Begum said in recent media interviews that Abase had stayed in a village where IS fighters are making a final stand against US-backed forces.
European countries have been grappling with what to do with foreign fighters detained in Syria by the Kurdish-led Syrian Democratic Forces, who have warned they may not be able to guard their jails once US troops leave.
The British government on Monday rebuffed US President Donald Trump's call to take back alleged UK jihadists captured in the war-ravaged country.
Trump had called on Britain, France, Germany and other European allies "to take back over 800 IS fighters that we captured in Syria and put them on trial".
Prime Minister Theresa May's spokesman said the fighters should instead face justice in places where they committed their crimes.
Shamima Begum, who now wants to return home after giving birth in a refugee camp in Syria last weekend, said the order was 'unjust'.