Mufti Nizamuddin Shamzai, who had called for a "jihad" or holy war against the United States after the invasions of Afghanistan and Iraq, was shot dead in May 2004 as he was driving to an Islamic school.
The suspect, Nafees Khan, was arrested in an overnight raid on a house, Farooq Awan, a senior police official, told Reuters.
Awan said Khan was one of six gunmen sought in connection with Shamzai's murder. "He was arrested after a witness in the case identified him from a picture in a police database," he added.
"Nafees Khan is a key suspect in the case, but we have no information on his links with any militant group."
Shamzai belonged to the hard-line Deobandi School of Islamic thought, which provided thousands of fighters for the Taleban militia, which took over neighbouring Afghanistan in the mid-1990s.
Shamzai led a delegation of Pakistani clerics and intelligence officials to Taleban supreme leader Mullah Mohammad Omar with a message from the government soon after the September 11, 2001 attacks on the United States.