Muhammed Hussain was convicted and sentenced to death in 2009 for murdering his senior officer Khadim Hussain in 2008, the BBC reported.
He was hanged at a jail in Punjab province early Thursday. All his petitions for mercy were rejected.
Shortly after the Pakistan Peoples Party came to power in 2008, it unofficially prohibited executions, the Press Trust of India reported.
Human Rights Commission of Pakistan Chair Zohra Yusuf told the BBC she did not think Hussain's execution marked a shift in the government's policy.
"Only recently the president asked the government to work on a draft law to abolish the death penalty," she said. "I hope this does not have implications for other cases. But I am worried. And I am worried about what happens after March when this government finishes its term."