The teenager was held after counter-terrorism police raided a house in Longsight, Manchester at about 8pm on Friday.
Police suspect the girl of “engaging in conduct in preparation for acts of terrorism”.
She has been bailed until May 28.
A spokesman for Greater Manchester Police (GMP) said: “As part of an ongoing investigation, on Friday, April 3, officers from the Tactical Aid Unit and North West Counter Terrorism Unit executed a warrant at a house in Longsight.
“A 16-year-old girl was arrested on suspicion of engaging in conduct in preparation for acts of terrorism and has been bailed until 28 May 2015.”
The arrest is not believed to be related to the nine people from Rochdale, stopped at the Turkey/Syria border this week.
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