The girl, who is from Muar, was arrested before she could board a Cairo-bound flight at Kuala Lumpur International Airport, The Malaysian Star reported.
A police official said the girl was planning to marry a 22-year-old Malaysian student in Cairo.
Both of them would then go to Istanbul before securing passage to Syria.
"We discovered that she had been in contact with two Malaysian militants based in Syria. We will investigate further to uncover the mastermind behind the recruitment of Malaysian girls for the IS," the official said.
"We will not allow Malaysia to be used as a training ground or hideout for terrorists and militants. Anyone in support or in league with any terrorist will be detained."
Intelligence sources said the girl's would-be husband is a student at Cairo's Al-Azhar University.
The girl had attempted to go to Cairo without her family's consent. She had even threatened to kill herself if her parents did not let her go.
The latest arrest brings the number of people linked to terrorism arrested in Malaysia to 68 since February 2013.
Among those arrested were navy and air force personnel and civil servants.
Last month, a young Malaysian couple, with their infant son, managed to elude the authorities to go to Syria to join the terror group.
"They went to Bangkok before taking a flight to Istanbul. They then entered Syria via a land route," a source said.
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