The unnamed 32-year-old Chechen national had been living in Maastricht in the southern Netherlands before taking her young son and daughter to ISIS capital Raqqa.
The father of the missing children named the pair as Luca, seven, and his sister Aysha, eight, and said they had been taken without his consent. The woman's two other children are believed to have been handed over to a relative before she left to join the terror group.
The missing woman, who has not yet been named, fled the Netherlands with two of her children last October, the Dutch prosecution's office confirmed this morning.
According to the Dutch newspaper, the children's father had previously reported his estranged wife to the police because he was concerned she was planning to travel to Syria.
Officers are said to have questioned the woman several times but she denied having intentions to join ISIS and investigators could find no evidence of concrete travel plans.
Shortly afterwards the woman vanished from Maastricht with two of the children, prompting Dutch officials to launch a major alert, leading to an international arrest warrant being issued.
Despite this the woman later took to Facebook to declare that she and her two children had arrived in the terrorists' de facto capital Raqqa, having used fake passports to travel across Europe.
After making the announcement of their arrival in Raqqa on Facebook last October, nothing has been heard from the trio since.