Abdur Rehman alias Abdul Rehman Sindhi, who was arrested yesterday in Karachi, was placed on the UN sanction list in 2012 for providing financial services to Al-Qaeda.
Individuals on the list are subject to a freeze on their assets, travel ban and arms embargo.
He was arrested during a joint operation of police and intelligence agencies in a congested residential quarter, Muqaddas Haider, a senior police officer told AFP.
Rehman is believed to have met Al-Qaeda founder Osama Bin Laden and his successor Ayman al-Zawahiri several times.
Rehman was a member of various Pakistan-based militant organisations before joining Al-Qaeda.
He served as a member of Al-Akhtar Trust, a banned Islamic charity, Jaish-e-Mohammad and Harkat-ul-Jihad Islami, all of which have also been proscribed internationally.