The 34-year-old woman, who cannot be named for legal reasons, wanted to live under Sharia law, Leeds Crown Court in northern England was told.
She abducted her children in October last year with the intention of going to Raqqa, where the ISIS jihadist group has set up its headquarters.
However, her husband and parents contacted the police and she was stopped in Istanbul by the Turkish authorities.
She admitted two counts of child abduction relating to her children, who were both under the age of 16.
“Raqqa is, and was in October 2015, the epicentre of a war zone. Further, it was, and presently remains, under the control of IS,” said judge Rodney Jameson.
“It is beyond dispute that IS enforce their will by the use of extreme force. Such force routinely includes mutilation, rape and murder. You are an intelligent and well-educated woman; you knew this.
“The fate of your children would have been either to have subscribed, fully and actively, as we have all seen in the appalling use of a young child in an IS propaganda video in recent days, to such behaviour, or to have suffered it themselves.”
The woman was born in Britain and spent her formative years in Pakistan before returning to northern England.
She became increasingly religious and gave up her job in finance in August last year, before attempting to take her children to Syria.
“This was a terrible betrayal of your responsibilities to your children,” said Jameson.
The judge jailed the woman for five years and four months.