It was not clear whether Pakistan would hand over Salam Rigi, a leader of the ethnic Baluch Sunni group Jaish al-Adl (Army of Justice), to Shi'ite-run Iran.
Rigi was seized by Pakistani authorities who were tipped off to his movements and intercepted the bus some 50 km from Quetta, the capital of Baluchistan, one security official said on condition of anonymity.
A second security official confirmed the arrest, saying Rigi offered no resistance.
Rigi is accused of involvement in suicide bombings in Iran and Pakistan, as well as sending fighters to the conflicts in Iraq and Syria.
He is the cousin of the movement's late leader Abdolmalek Rigi, who was hanged by Iran in 2010, and had taken over many of his relative's leadership roles.
Jaish al-Adl, a Sunni Muslim rebel group, operates in predominantly Shi'ite Muslim Iran's Sistan-Baluchistan province, which borders Pakistan.
The impoverished border area has been a hotbed of rebellion and is also rife with drug and arms traffickers.