Following US pressure, Pakistan has added Jamaat-ud-Dawa led by 2008 Mumbai attack mastermind Hafiz Saeed and Haqqani network in the list of proscribed organisations.
The move comes ahead of US President Barack Obama's visit to India.
US officials, led by secretary of state John Kerry, told Pakistan to stop making a distinction between "good militants" and "bad militants" after the Taliban attack on an army-run school in Peshawar that killed 150 people, of whom 131 were school children.
After the ban, the assets of these groups will be frozen.
The Haqqani network, founded by Jalaluddin Haqqani, has been blamed for the Indian embassy bombing in Afghanistan in 2008 that left 58 people dead, a 2011 attack on the US embassy in Kabul, and several truck bombing attempts in Afghanistan.