The 14-year-old girl named Sarah "reported to the police this morning accompanied by a relative", Rotterdam police's Roland Ekkers said.
"She's been taken into custody with a hearing against her to start soon," he told AFP.
Sarah apparently posted the message that landed her in hot water on social network Twitter today morning.
"hello, my name's Ibrahim and I'm from Afghanistan. I'm part of Al Qaida and on June 1st I'm gonna do something really big bye," read the message, which has since been deleted together with her account.
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Dutch public broadcaster NOS said Sarah, whose tweet earned her thousands of new followers, then furiously tried to rectify the situation.
She tweeted: "I'm really sorry. I'm really scared now. I made a joke, please... I'm just a girl."
Another tweet, published by the NOS read: "I'm not going to tell my parents. They'll tell me to delete my acc (account) omg (oh my God) that will be the end of my life".
"I always wanted to be famous, but I meant like (teen idol) Demi Lovato famous, not Osama bin laden famous."
It is not sure how long Sarah will still be under arrest, he added. "We would like to find out what her motives were.