The chopper was going from Rawalpindi to Gilgit in the north to evacuate a "critical soldier" when it crashed near Mansehra district in Khyber-Pakhtunkhwa province.
Military sources confirmed the crash and said 12 people including a team of army doctors, paramedics, pilots and crew were killed.
"Apparently (bad) weather seems to be cause of crash. Rescue operation is going on," said the military officials.
Earlier, an MI-17 helicopter crashed in May near Gilgit when it was taking a group of diplomats on trip.