Among Saturday's protesters were prominent activists such as Narges Mohammadi, Bahareh Hedayat and Vida Rabbani who slammed the execution of the protesters.
Anti-government unrest broke out in Iran in September 2022 following the death in custody of Mahsa Amini, who was detained by the country's "morality police" for not wearing her hijab "correctly".
This led to large-scale demonstrations across the country.
Hedayat urged the detainees to "prepare a political agenda that will lead to the victory of the protesters", according to BBC Persian.
Mohammadi said the executions of the three political prisoners will spur on further anti-government protests which began after the death of Amini but have mostly fizzled out following a brutal crackdown by authorities.
The three political prisoners who were executed on Friday were charged with the deaths of two Basij members and a police officer during protests in Isfahan in November 2022, as well as creating groups that "undermined Iran’s national security".
The executions drew criticism from UN experts on the Human Rights Council who said they were "deeply disturbed that these men have reportedly been subjected to torture or other forms of ill-treatment to extract forced confessions".
Human rights groups, such as the Center for Human Rights in Iran (CHRI), have labelled the ongoing executions in Iran as a "killing spree", with executive director of CHRI Hadi Ghaemi stating "The Islamic Republic’s death machine is in high gear".