Naamen Maziche, who is of French origin, was described by the state-run media as a "prominent operative of Al Qaeda responsible for external operations" and was on a list of "most wanted persons".
Reports said he was arrested by law enforcing agencies during an operation on the Pakistan-Iran border. They did not say when he was arrested.
Maziche was reported to be a close associate of al-Qaeda leader Younis al-Mauritani, reports said.
Some media reports described Maziche as an al-Qaeda operative with links to European jihadi groups.
Younis al-Mauritani had been appointed by Osama bin Laden as commander of operations in Africa. Al-Mauritan and three of his associates were arrested by Pakistani security agencies in the southwestern city of Quetta last year.
After al-Mauritani's arrest, Maziche moved to Iran, the reports said.
Al-Mauritani had reportedly told interrogators that Maziche had moved to Iran with some of his associates en route to Africa.