The attack on the madrassa brings back memories of the 2014 terrorist massacre at the Army Public School in Peshawar.
The insurgent outfit may attempt to target political and religious leaders in Quetta and Peshawar, according to the warning.
Gunmen killed at least six people in Balochistan, while a improvised explosive device blast killed six security personnel in Waziristan.
Tehran's efforts to stoke upheaval in Pakistan are part of its overall plan to destablise and dominate the region, said a top leader of the Iran-based militant group Jaish al-Adl.
As Islamabad seeks potential assistance from Washington, recent tensions between the United States and China may offer an opportunity for Pakistan to improve its economy.
The Federal Board of Revenue is continuing to break up networks and arrest suspected financial backers of militant outfits.
'With the alliance, the insurgency here is likely to escalate here in coming days,' said one defence analyst.
In Khyber Pakhtunkhwa, officials deregistered 3,851 of 5,931 NGOs for failing to provide their funding and project details.
The group is named for Abdul Rashid Ghazi, an Islamic fundamentalist leader of Lal Masjid in Islamabad who was killed during a government siege of the complex in July 2007.
The suspects were planning to carry out suicide attacks on the police stations and police patrol vans.