The children, many of them under five years old, are enduring “dire conditions” in desolate camps or have been displaced multiple times in the complex battle zone, the group added.
The international rights group urged the UK government to bring the British children home, saying they are in danger as the conflict has already overtaken at least one displaced camp holding foreigners.
Ain Issa camp, located around 35km (22 miles) from the Turkish border, was home to 12,000 people including several Britons but has now been disbanded after it came under fire. The location of most of the inhabitants is unknown.
There are also concerns that access will be lost after Kurdish-led forces, abandoned by their US allies, struck a deal with the Syrian regime.
Damascus has now sent troops to northern Syria and may take over administration of the camps, which were previously under Kurdish control,
Last week, foreign secretary Dominic Raab told the Commons that the UK would be willing to return home unaccompanied children or orphans in Syria but did not say what would happen to those who are still with their parents.
The BBC discovered at least three British orphans, named as Amira, Heba and Hamza, in Ain Issa earlier this month. The trio have since been moved by Kurdish-led forces to Raqqa, when Ain Issa came under fire.
But Sonia Kush, Syria director of Save the Children, argued that all British children should be brought home, whether they are with their parents or not. Until Monday’s report, previous estimates put the total at just over 35 British children in northern Syria.
“There has been some attention paid to British orphans but the vast majority of UK children trapped in Syria are under five years old, are with their mothers and are in need of urgent repatriation. It is important that they be seen as children and prioritised,” Ms Kush told The Independent.
“The children should not be separated from their mothers, which is an idea that is harder for governments to handle. But we have confidence in the judicial and legal process back home.”
Alison Griffin, Save the Children’s director of conflict and humanitarian campaigns, stressed that older children who lived under Isis likely witnessed appalling acts of brutality, including beheadings, and so were in need of urgent physiological care.
“Their short lives have been full of violence and fear but with the right care they can bounce back, recover and amaze us. They deserve that chance, no matter what they’ve been dragged into by the decisions of adults,” she said.
“The camps with the majority of foreign women and children have not yet been reached by fighting and remain under the control of the Kurdish authorities. The time to act is now,” she added.
Turkish president Recep Tayyip Erdogan launched a controversial offensive to repel Kurdish-led Syrian Democratic Forces (SDF) and create a 30km-deep buffer zone along its border.
After US president Donald Trump announced the withdrawal of American troops, who had been fighting alongside Kurdish forces against Isis, the SDF struck a deal with the Assad regime to defend the border.
Fighting continues in some areas, despite a US-brokered temporary ceasefire, which is due to expire on Tuesday.
Save the Children warned the potential administrative takeover of the Syrian regime would likely halt access international rights groups have to the camps, as the NGOs are not registered with the Syrian regime.
It would also likely complicate the repatriation process because it would mean the UK government would have to directly negotiate with Damascus rather than the Kurds.
There are also concerns that British children have gone missing in northern Syria as the frontline has moved.
When the inhabitants of Ain Issa fled, among them were at least two British women and their children: Tooba Gondal from east London, who joined Isis in Syria and worked to recruit others to follow her, and Zara Iqbal, also from east London.
The pair are now believed to be in a camp run by Turkish-backed Syrian forces after they were captured while escaping shelling.
The location of the rest of the camp’s inhabitants is unknown.
Kurdish doctors who run clinics in the camps said countries like the UK were running out of time, as the camps were becoming more volatile.
Aid workers in Al-Hol camp, home to some 70,000 people, including 11,000 foreigners affiliated with Isis, told The Independent that dozens of families have attempted to break free from the camp at least five times over the past few days.
Similar concerns were raised about Roj camp, which is home to 950 foreigners including Shamima Begum, who was part of the “Bethnal Green trio” of girls who joined Isis.
“From the outset, we have asked all countries to receive their nationals who are affiliated with Isis but unfortunately this has been repeatedly ignored by most countries and only heeded by a few,” said Dr Ahmed Sheikhmus, Kurdish Red Crescent coordinator in Roj.
“We have no objection to handing foreign nationals to their governments, now is the time,” he added.
We have no objection to handing foreign nationals to their governments, now is the time
Dr Ahmed Sheikhmus, medical coordinator Roj camp for the displaced
“In relation to unaccompanied minors or orphans, assuming that they would represent no security threat … we would be willing to see them returned home if that can be done in a safe way given the situation on the ground,” he said.
Save the Children’s team, meanwhile, said they spoke to one British mother with two young children – a baby and an under-five – in one of the camps who said there were 15 British citizens there.
The mother said she and her family made a traumatic escape from “hell” in Baghouz and, along with her children and sister, they ended up sleeping in the open desert as they fled. Her youngest baby nearly died from bronchiolitis when they arrived at the camp earlier this year.
“She accepted that she would face investigation in the UK but said she felt that in Syria no one would ever hear her case,” the group wrote.
“She told us that she was scared to be in the camps and very afraid of what would happen to her children.”