The demonstrations urged the government to take action against the United States and Israel, whom they accuse of carrying out the operation against Mohsen Fakhrizadeh.
"No peace, no surrender - war with the United States and death to Israel," the protesters chanted in a demonstration outside the Supreme council for National Security in Tehran on Friday.
Mohsen Fakhrizadeh, dubbed by Israel as the "father" of Iran's nuclear programme, died on Friday after being seriously wounded when assailants targeted his car and engaged in a gunfight with his bodyguards outside Tehran, according to Iran's defence ministry.
The Islamic republic's supreme leader Ayatollah Ali Khamenei called for the perpetrators to be punished, while President Hassan Rouhani stressed the country would seek its revenge in "due time" and not be rushed into a "trap".
"They are thinking of creating chaos, but they should know that we have read their hands and they will not succeed," Rouhani said.
He pinned the blame for the killing on "the wicked hands of the global arrogance, with the usurper Zionist regime as the mercenary".
Iran generally uses the term "global arrogance" to refer to the US.
"This barbaric assassination shows that our enemies are in stressful weeks, during which they feel... their pressure declining, the global situation changing," the Iranian president added.
"The nation of Iran is smarter than to fall in the trap of the conspiracy set by the Zionists."
The assassination comes less than two months before US President-elect Joe Biden is due to take office, after a tumultuous four years of hawkish foreign policy in the Middle East under President Donald Trump.
Trump unilaterally withdrew in 2018 from a multilateral nuclear deal with the Islamic republic, which sought to contain its atomic ambitions, and has re-imposed crippling sanctions. But Biden has signalled his administration may be prepared to rejoin the accord.