The International Security Assistance Force declined to identify the senior al Qaeda man, saying it was not releasing more details.
"It`s part of an ongoing operation," Army Maj. Tim James, spokesman for ISAF`s joint command in Kabul, was quoted as saying by CNN.
The operation comes a month after US commandos killed al Qaeda chief bin Laden in a raid in Abbottabad, Pakistan.
The man was arrested along with two others described as "associates," according to ISAF, during a raid on Wednesday in the northern province of Balkh, an insurgent stronghold that borders Uzbekistan.
In a statement posted on its website, ISAF released few details about the arrest, saying only that it is "suspected he was with bin Laden in Afghanistan in 2001."
He was captured during an overnight operation after he was tracked to a compound in Nahr-e Shahi, the statement said.
The arrest follows another a day earlier in the same area of a suspected al Qaeda-linked militant believed responsible for last week`s suicide attack at a provincial governor`s office that killed an Afghan police commander and wounded a German general, according to an ISAF operational update posted on its website.
NATO said he is one of several senior al-Qaida and Taliban insurgents captured in the province since February. It said a total of 35 people associated with al-Qaida and the Taliban have been captured in Balkh during that period.