Law minister Zahid Hamid presented the 28th Constitutional Amendment Bill in the Senate last week but it could not be voted as the required number of lawmakers were not present in the House.
The Senators from the both sides of the aisle discussed the bill in detail before voting.
Finally, the House passed the bill with 78 Senators supporting it while only three opposed the amendment in the House of 104. The amendment was thus adopted by the required two-thirds majority.
The bill was opposed by three Senators of Pakhtunkhwa Milli Awami Party.
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The military courts were first set up in January 2015 for a two year term after a constitutional amendment following a terror attack on an army-run school in Peshawar in December 2014 that killed over 150 people, mostly students.
Since their expiry in January, government has been trying to bring the political parties around the idea of another tenure for military courts.
The military courts awarded death sentence to 161 militants and so far only 21 have been executed.
The military courts work in secrecy due to fear of backlash by militants. Rights group have slammed the military courts.
The courts were given 275 cases during two years and they sentenced 161 terrorists to death, whereas another 116 were given varying jail terms, mostly life sentences.
Pakistan this year witnessed a surge in terror attacks.
Over 80 people were killed after an Islamic State (IS) suicide bomber blew himself up at the Lal Shahbaz Qalander dargah in Sehwan on February 18. A suicide bomber attacked a protest rally outside the Punjab assembly in Lahore on February 13, killing 14 people and injuring dozens.