The former president and other top former Tehran officials are wanted in connection with the 1994 bombing of a Jewish charity in Argentina that killed 85 people.
Judge Rodolfo Canicoba Corral has asked the government of Iran as well as Interpol to hand over the former president on a warrant issued for "crimes against humanity."
The crimes relate to the bombing attack of the Argentine Jewish Mutual Association, a Jewish charities federation office, in which 85 people died and 300 were injured.
"A close analysis at the request of the national prosecutor resulted in this (warrant)," he said.
No one has ever been convicted for the bombing, which occurred on the
morning of July 9, 1994.
Argentinean President Nestor Kirchner has taken up the cause, as he has in many human rights cases stemming from Argentina's 1976-1983 military dictatorship.
President Kirchner has said "grave failures of justice" had prevented the resolution
of the case.
Iranian response
The Iranian government has vehemently denied any involvement in the attack following repeated accusations by Jewish community and other leaders.
Iran's leading diplomatic envoy in Buenos Aires, said his government would oppose any efforts to detain Rafsanjani or its nationals.
Mohsen Bahvarvand, Iran's charge d'affaires in Buenos Aires, called the case politically motivated.