Mubashir Ejaz Ahmad, 27, and his mother were killed in G-11 area last night, his brother Mujadid Ejaz Ahmad said.
"Police has registered a case and launched investigation but so far they have no idea who killed them," Ahmad said.
"We do not have enmity with anyone," he said, adding that the possibility of extremists' involvement in the murder cannot be ruled out.
Police officials were not available for comments.
Mubashir was a qualified Electronic Engineer and was teaching at Muhammad Ali Jinnah University in Islamabad.
Some 1.5 million Ahmadis live across the country.