The demonstration were organised after Friday prayer by Jamat-e-slami (JI), a right wing party which is heavily influenced by the Muslim Brotherhood.
The biggest rally of around 1,000 people was taken out in southern coastal city of Karachi.
JI local leader Muhammad Hussain Mahanti condemned the killing of "innocent people" by the Egyptian army while addressing the protesters.
He also demanded restoration of the ousted president.
Protests were also held in other cities where people raised slogans against the US.
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Yesterday, the lower house of parliament and foreign ministry expressed deep concern over the use of force "against unarmed civilians" and urged all sides to show restraint.
At least 38 people were killed in Egypt today as thousands of Muslim Brotherhood supporters thronged streets and clashed with security forces in Cairo, Ismailiya, Damietta, Alexandria and elsewhere.
The protesters demanded an end to military-backed government and reinstatement of 62-year-old Morsi, who was ousted by the army on July 3 after countrywide protests.