Syed Sibtain Kazmi, 57, from Bradford, is accused of being involved in the killing of Maulana Azam Tariq in 2003.
Mr Tariq, the leader of the banned Sipah-e-Sahaba group, was shot dead when his vehicle was attacked by gunmen in Islamabad during a spate of violence between Shia and Sunni groups.
Mr Kazmi, was arrested at Islamabad airport, a spokesperson for Pakistan's Federal Investigation Agency said.
Mr Kazmi told the BBC in August he was the cleric who granted an Islamic divorce to alleged "honour killing" victim Samia Shahid.
Ms Shahid, 28, from Bradford, died while visiting relatives in Pakistan in July 2016.
Syed Sibtain Kazmi is a Shia cleric from Pakistan who has spent years leading prayers at a number of British mosques - most recently in Bradford.
He was wanted in Pakistan in connection with the 2003 shooting of a leader of a banned Sunni organisation - linked to attacks on Shia Muslims.
Today he was arrested at Islamabad airport on route to the UK.
Kazmi's supporters have, in the past, denied the allegations against him.
A British-based imam has been arrested in Pakistan on suspicion of murder.