The decision was taken after a marathon consultative session of government and opposition politicians.
The meeting was chaired by Speaker National Assembly Sardar Ayaz Sadiq.
"We have agreed to reestablish military courts for a period of two years, considering it is an issue of national importance," Sadiq told reporters after the talks.
He said that the Constitution would be amended to introduce the military courts.
Finance minister Ishaq Dar, who was also part of the talks, said that the decision to revive military courts was made in view of the fact that the country is fighting a war against terrorism.
PPP leader Aitzaz Ahsan said that the opposition had agreed to the proposal conditionally after consultation.
"The government has agreed to four of the nine demands put forth by Pakistan People's Party (PPP)," he said.
Pakistan Tehreek-e-Insaf's Shah Mehmood Qureshi said the court would not target anyone for his religious beliefs.
The religious parties still have some reservations over the language of the proposed law which would be addressed in the final draft, said Sadiq.
The military courts awarded death sentence to 161 militants and so far only 21 have been executed.
Army had demanded to revive the courts for another two years to try more militants and punish them.
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