Activists of the Jamaat-ud-Dawah and Kashmiri groups organised protests against the execution of Afzal Guru in several Pakistani cities while the administration of Pakistan-occupied Kashmir announced three days of mourning.
Dozens of JuD activists joined a protest held outside the National Press Club in Islamabad hours after Guru was hanged and buried in Delhi's Tihar Jail on Saturday morning.
Similar protests were organised by the JuD in Lahore and Karachi.
JuD chief Hafiz Mohammad Saeed, a mastermind of the 2008 Mumbai attacks, claimed Guru's execution amounted to "judicial terrorism".
In a statement issued in Lahore, he said: "We strongly condemn the hanging of Afzal Guru. It is judicial terrorism and it cannot be approved of".
Saeed claimed Guru was hanged because the Indian government wanted to divert the people's attention from "internal conflicts".
He contended that the "freedom movement" in Jammu and Kashmir would continue as the execution had angered people.
In Muzaffarabad, the capital of PoK, about 400 members of Kashmiri groups joined a rally to protest the execution of Guru, who was convicted for his role in a terrorist attack on the Indian parliament in 2001.
The demonstrators burnt Indian flags and shouted slogans like "Down with India" and "We will continue Afzal Guru's mission".
The protest was organised by Pasban-e-Hurriyat, which represents Kashmiris who migrated from Jammu and Kashmir.
Hurriyat leader Uzair Ahmad Ghazali said protestors will join a sit-in outside the United Nations office in Muzaffarabad on Monday.
PoK government spokesman Shaukat Javed Mir said there would be three days of mourning in the region and the flag would fly at half-mast during this period.
Officials claimed Guru was tried and executed under "draconian laws".
Guru was found guilty of conspiring with and sheltering the terrorists who attacked parliament in December 2001