The "three hardcore terrorists" were executed at High Security Prison in Sahiwal district of Punjab province, army said in a statement.
"These terrorists were involved in committing heinous offences relating to terrorism, including attacks on Armed Forces and Law Enforcement Agencies," it said.
The militants were associated with the Pakistani Taliban and a second extremist group named Harkat-ul-Jihad e-Islami, it said.
The convicts identified as Said Zaman Khan, Shawaleh and Muhammad Zeeshan were tried and convicted by special military courts.
These courts were set up for two years in January 2015 and became dysfunctional from January 7, 2017. The courts were set up 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.
The military court awarded death sentence to 161 militants and so far only 21 have been executed.