Sajid Javid said females account for a significant proportion of around 900 individuals who left the UK to travel to territory held by extremist groups in Syria and Iraq.
Some may have taken their offspring with them, he said, while others may have had children whilst overseas.
Mr Javid confirmed a child born to a British-born mother anywhere in the world was also British, so long as the woman was British at the time of the birth.
His remarks came as he was quizzed by MPs about the case of Shamima Begum, who left east London to join IS in 2015.
Earlier this month, she declared she wanted to come back to the UK with her child.
But in an effort to block her return, Mr Javid stripped Ms Begum of her British citizenship.
The Home Secretary said he had taken the child’s interests into account when making the decision.
While repeatedly declining to address the specific case, he told the Commons Home Affairs committee: “I can confirm that if you are a British-born mother and you have a child anywhere in the world, that child, so long as you are British at the point that child is born, is British.”
Asked whether there was any plan for Ms Begum’s son, Mr Javid said: “Sadly, there are probably many hundreds of children that have been born to foreign fighters.
“As I mentioned, 900 people have gone out. We don’t have a breakdown between men and women, but a significant proportion have been female foreign fighters.
“Some of them may have taken children with them, and many of them would have had children out there whilst in Syria and working with Daesh.”
He said it would be “incredibly difficult” to facilitate the return of a child from Syria.
“If it’s possible somehow for a British child to be brought to a place where there is a British consular presence, Turkey for example, in those circumstances I guess potentially it is possible to arrange some sort of help with the consent of the parent,” Mr Javid told the committee.
“But inside Syria, there is no British consular presence.”
The 900 figure relates to the estimated number of people “of national security concern” who travelled from the UK to engage in the conflict in Syria and Iraq.
Of those, approximately 20 per cent have been killed overseas, while around 40 per cent have returned to the UK.
A “significant proportion” of returnees are assessed as no longer being of a security concern, according to the Home Office.
Mr Javid hit back at suggestions his decision to revoke Ms Begum’s citizenship was politically motivated.
He said: “This power has been used by successive home secretaries and governments of different political persuasions.
“These decisions are never political in any way. It’s all about the job the Home Secretary has to protect the British public.
“This is not some sort of new national security tool that I just invented or just rolled out. It goes back over 100 years.”
He also denied he was attempting to “export” a problem created in Britain.
It is thought the decision was made in the belief Ms Begum qualifies for Bangladeshi citizenship, but authorities there have said they will not allow her into the country.
The British Nationality Act 1981 provides the Home Secretary with the power to strip someone of their citizenship if they are satisfied such action is “conducive to the public good”.
Mr Javid acknowledged that it “might be a blunt tool”, adding: “It should only be used in the most exceptional circumstances and cannot be used lightly.”
He said many people “with similar heritage to mine” have “absolutely supported” his decision.
Mr Javid added: “No-one in the British Muslim community, and I include myself in that, wants to see people taking the name of their great peaceful religion and twisting it for their own wicked means.”