A 14-year-old boy from Blackburn, Lancashire, was detained on 2 April following the examination of a number of electronic devices, police said.
He was questioned on suspicion of preparing for an act of terrorism.
A 16-year-old girl was subsequently arrested at a house in Longsight, Manchester, on 3 April on suspicion of engaging in conduct in preparation for acts of terrorism.
Both teenagers were bailed until 28 May.
The investigation involved officers from the North West Counter-Terrorism Unit, the Tactical Aid Unit, Greater Manchester Police and Lancashire Constabulary.
Police said the arrests were not linked to the detention of nine people from Rochdale on the Turkey-Syria border earlier this week.
The group, including five adults and four children, was seized in Hatay on 1 April.
Their intention in travelling to the region, where areas are controlled by Islamic State (IS) militants or an al-Qaeda affiliate, is being investigated.
Two teenagers have been arrested on suspicion of terrorism offences.